Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xbn Working: n-0-138.cluster.ucsf.bkslab.org:/scratch/xiaobo/13323/xbn-8058097.40 Result: /scratch/xiaobo/13323/xbn-8058097.40 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbn Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xbn mkdir: created directory `/scratch/xiaobo/13323' mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40' /scratch/xiaobo/13323/xbn-8058097.40 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working' mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/protonate' Storing results in /scratch/xiaobo/13323/xbn-8058097.40/finished Working in /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 /scratch/xiaobo/13323/xbn-8058097.40/working/protonate /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Using inputs as protomers/tautomers. No processing done 485 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/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Bulk generating 3D conformations all protomers in /scratch/xiaobo/13323/xbn-8058097.40/working/3D mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/13323/xbn-8058097.40/working/protonate/xbn-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 ZINC001290025272 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building' mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290025272 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/1 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290025272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025272 none Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 49, 49, 35, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 49, 35, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/2 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290025272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025272 none Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 49, 49, 35, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 49, 35, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025272 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/finished' Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 Building ZINC001290025272 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290025272 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 1) grep: /scratch/xiaobo/13323/xbn-8058097.40/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: Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290025272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025272 none Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 49, 49, 35, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 49, 35, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 2) grep: /scratch/xiaobo/13323/xbn-8058097.40/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: Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290025272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025272 none Cc1nn(C)cc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', '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, 1, 8, 8, 5, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 49, 49, 35, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 49, 35, 35, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025272 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025272 Building ZINC001290025299 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290025299 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/3 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/3' -> `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)c2cncnc2O)C1) `ZINC001290025299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001290025299 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)c2cncnc2O)C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 45, 45, 45, 50, 50, 45, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 29, 29, 45, 50, 50, 100, 29, 29] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/4 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/4' -> `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)c2cncnc2O)C1) `ZINC001290025299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001290025299 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)c2cncnc2O)C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 33, 33, 33, 33, 33, 47, 47, 47, 50, 50, 47, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 33, 47, 50, 50, 100, 33, 33] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 271 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025299 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 Building ZINC001290025299 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290025299 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 3) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)c2cncnc2O)C1) `ZINC001290025299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001290025299 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)c2cncnc2O)C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 45, 45, 45, 50, 50, 45, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 29, 29, 45, 50, 50, 100, 29, 29] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 4) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)c2cncnc2O)C1) `ZINC001290025299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001290025299 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)c2cncnc2O)C1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 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, 3, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 33, 33, 33, 33, 33, 47, 47, 47, 50, 50, 47, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 33, 33, 47, 50, 50, 100, 33, 33] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 271 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025299 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025299 Building ZINC001290025348 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025348 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/5 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/6 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/7 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/7' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/8 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/8' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025348 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 Building ZINC001290025348 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025348 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 5) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 6) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 7) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 8) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025348 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 Building ZINC001290025348 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025348 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 5) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 6) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 7) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 8) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025348 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 Building ZINC001290025348 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025348 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 5) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 6) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 7) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 8) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025348.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025348 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 21, 21, 21, 14, 14, 14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 21, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001290025348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025348 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025348 Building ZINC001290025349 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025349 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/9 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/10 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/11 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/11' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/12 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/12' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025349 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 Building ZINC001290025349 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025349 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 9) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 10) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 11) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 12) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025349 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 Building ZINC001290025349 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025349 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 9) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 10) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 11) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 12) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025349 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 Building ZINC001290025349 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025349 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 9) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 10) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 11) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 22, 22, 22, 15, 15, 15, 15, 10, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 22, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 12) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001290025349.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290025349 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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', '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, 10, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 13, 13, 13, 13, 10, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 20, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50] 50 rigid atoms, others: [48, 50, 49, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 51, 52, 53, 54]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025349 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025349 Building ZINC001290025397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/13 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/13' -> `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]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/14 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/14' -> `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]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 22, 22, 22, 22, 22, 37, 37, 38, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/15 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/15' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/16 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/16' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21] 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, 54]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 Building ZINC001290025397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 13) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 14) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 22, 22, 22, 22, 22, 37, 37, 38, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 15) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 16) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21] 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, 54]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 Building ZINC001290025397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 13) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 14) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 22, 22, 22, 22, 22, 37, 37, 38, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 15) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 16) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21] 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, 54]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 Building ZINC001290025397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290025397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 13) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 14) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1) `ZINC001290025397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 22, 22, 22, 22, 22, 37, 37, 38, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 15) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 38, 38, 39, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 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, 54]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 16) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2CC[N@@](C)CC2)C1) `ZINC001290025397.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290025397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock 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', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21] 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, 54]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025397 Building ZINC001290025488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290025488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/17 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1) `ZINC001290025488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025488 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 13, 13, 13, 13, 13, 30, 30, 30, 48, 48, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 30, 48, 48, 48, 48, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/18 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1) `ZINC001290025488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025488 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 13, 13, 13, 13, 13, 30, 30, 30, 48, 48, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 30, 48, 48, 48, 48, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 Building ZINC001290025488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290025488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 17) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1) `ZINC001290025488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290025488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025488 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 13, 13, 13, 13, 13, 30, 30, 30, 48, 48, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 30, 48, 48, 48, 48, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 18) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1) `ZINC001290025488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290025488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290025488 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1C[C@@H](NC(=O)CCn2cccn2)C1 NO_LONG_NAME dock 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', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 13, 13, 13, 13, 13, 30, 30, 30, 48, 48, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 30, 48, 48, 48, 48, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290025488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290025488 Building ZINC001290036150 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290036150 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/19 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290036150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290036150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290036150 none CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 22, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 31, 31, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/20 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290036150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290036150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290036150 none CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 22, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 31, 31, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290036150 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 Building ZINC001290036150 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290036150 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 19) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290036150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290036150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290036150 none CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 22, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 31, 31, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 20) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290036150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290036150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290036150 none CCn1ncc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 31, 31, 31, 31, 31, 22, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 50, 50, 50, 50, 50, 31, 31, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290036150 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290036150 Building ZINC001290039004 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290039004 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/21 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/21' -> `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)CO[C@@H]2CCOC2)C1) `ZINC001290039004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290039004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039004 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 16, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 38, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/22 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/22' -> `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)CO[C@@H]2CCOC2)C1) `ZINC001290039004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290039004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039004 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 16, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 38, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290039004 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 Building ZINC001290039004 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290039004 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 21) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@@H]2CCOC2)C1) `ZINC001290039004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290039004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039004 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 16, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 38, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 22) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@@H]2CCOC2)C1) `ZINC001290039004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290039004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039004 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 16, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 38, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290039004 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039004 Building ZINC001290039005 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290039005 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/23 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/23' -> `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)CO[C@H]2CCOC2)C1) `ZINC001290039005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290039005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039005 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 17, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 17, 17, 38, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/24 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/24' -> `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)CO[C@H]2CCOC2)C1) `ZINC001290039005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290039005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039005 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 37, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290039005 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 Building ZINC001290039005 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290039005 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 23) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@H]2CCOC2)C1) `ZINC001290039005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290039005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039005 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 17, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 17, 17, 38, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 24) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@H]2CCOC2)C1) `ZINC001290039005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290039005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290039005 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 37, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290039005 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290039005 Building ZINC001290043532 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290043532 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/25 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290043532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043532 none CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 34, 31, 34, 34, 31, 31, 18, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 38, 34, 34, 34, 31, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 210 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/26 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290043532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043532 none CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 33, 32, 33, 33, 32, 32, 21, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 38, 33, 33, 33, 32, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290043532 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 Building ZINC001290043532 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290043532 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 25) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290043532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043532 none CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 34, 31, 34, 34, 31, 31, 18, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 38, 34, 34, 34, 31, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 210 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 26) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290043532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043532 none CCC(=O)N[C@@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 33, 32, 33, 33, 32, 32, 21, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 38, 33, 33, 33, 32, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290043532 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043532 Building ZINC001290043533 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290043533 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/27 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290043533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043533 none CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 30, 31, 31, 30, 30, 18, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 36, 31, 31, 31, 30, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/28 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290043533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043533 none CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 30, 27, 30, 30, 27, 27, 18, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 34, 30, 30, 30, 27, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290043533 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 Building ZINC001290043533 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290043533 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 27) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290043533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043533 none CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 30, 31, 31, 30, 30, 18, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 36, 31, 31, 31, 30, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 28) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290043533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290043533 none CCC(=O)N[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 30, 27, 30, 30, 27, 27, 18, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 34, 30, 30, 30, 27, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290043533 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043533 Building ZINC001290043614 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290043614 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/29 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290043614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290043614 none CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 36, 36, 36, 15, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 47, 47, 36, 15, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/30 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290043614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290043614 none CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 50, 32, 32, 32, 14, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 44, 44, 32, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290043614 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 Building ZINC001290043614 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290043614 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 29) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290043614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290043614 none CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 36, 36, 36, 15, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 47, 47, 36, 15, 15, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 30) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290043614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290043614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290043614 none CCS(=O)(=O)CC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 50, 32, 32, 32, 14, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 44, 44, 32, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290043614 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290043614 Building ZINC001290056861 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056861 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/31 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/31' -> `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]2CC[C@H]2C(N)=O)C1) `ZINC001290056861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056861 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 37, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/32 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/32' -> `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]2CC[C@H]2C(N)=O)C1) `ZINC001290056861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056861 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 38, 38, 49, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 17, 17, 38, 50, 50, 50, 50, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056861 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 Building ZINC001290056861 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056861 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 31) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@H]2C(N)=O)C1) `ZINC001290056861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056861 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 37, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 32) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@H]2C(N)=O)C1) `ZINC001290056861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056861 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 38, 38, 49, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 17, 17, 38, 50, 50, 50, 50, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056861 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056861 Building ZINC001290056862 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056862 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/33 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/33' -> `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]2CC[C@@H]2C(N)=O)C1) `ZINC001290056862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056862 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 19, 19, 43, 50, 50, 50, 50, 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/34 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/34' -> `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]2CC[C@@H]2C(N)=O)C1) `ZINC001290056862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056862 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 19, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 19, 19, 43, 50, 50, 50, 50, 50, 50, 7, 7] 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: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056862 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 Building ZINC001290056862 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056862 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 33) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@@H]2C(N)=O)C1) `ZINC001290056862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056862 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 19, 19, 43, 50, 50, 50, 50, 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 34) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@@H]2C(N)=O)C1) `ZINC001290056862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056862 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 19, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 19, 19, 43, 50, 50, 50, 50, 50, 50, 7, 7] 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: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056862 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056862 Building ZINC001290056863 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056863 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/35 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/35' -> `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]2CC[C@@H]2C(N)=O)C1) `ZINC001290056863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056863 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 17, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 38, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/36 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/36' -> `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]2CC[C@@H]2C(N)=O)C1) `ZINC001290056863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056863 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 37, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056863 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 Building ZINC001290056863 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056863 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 35) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@@H]2C(N)=O)C1) `ZINC001290056863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056863 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 17, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 38, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 36) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@@H]2C(N)=O)C1) `ZINC001290056863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056863 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 37, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 37, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056863 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056863 Building ZINC001290056864 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056864 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/37 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/37' -> `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]2CC[C@H]2C(N)=O)C1) `ZINC001290056864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056864 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 20, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 20, 20, 45, 50, 50, 50, 50, 50, 50, 7, 7] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/38 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/38' -> `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]2CC[C@H]2C(N)=O)C1) `ZINC001290056864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056864 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 20, 20, 42, 50, 50, 50, 50, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056864 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 Building ZINC001290056864 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290056864 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 37) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@H]2C(N)=O)C1) `ZINC001290056864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290056864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056864 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 20, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 20, 20, 45, 50, 50, 50, 50, 50, 50, 7, 7] 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 38) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@H]2C(N)=O)C1) `ZINC001290056864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290056864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290056864 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](CNC(=O)[C@@H]2CC[C@H]2C(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', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 20, 20, 42, 50, 50, 50, 50, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290056864 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290056864 Building ZINC001290057532 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290057532 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/39 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290057532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290057532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290057532 none COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/40 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290057532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290057532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290057532 none COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290057532 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 Building ZINC001290057532 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290057532 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 39) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290057532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290057532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290057532 none COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 40) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290057532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290057532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290057532 none COc1nccc(C(=O)NC[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290057532 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290057532 Building ZINC001290060839 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290060839 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/41 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290060839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290060839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290060839 none Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 11, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/42 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290060839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290060839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290060839 none Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 10, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 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: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290060839 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 Building ZINC001290060839 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290060839 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 41) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290060839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290060839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290060839 none Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 11, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 42) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290060839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290060839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290060839 none Cn1cncc1CCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 10, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 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: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290060839 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290060839 Building ZINC001290068163 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290068163 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/43 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290068163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290068163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290068163 none CN(C)CCCC(=O)NC[C@H]1C[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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 33, 24, 11, 11, 11, 10, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 44, 44, 33, 33, 24, 24, 11, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 50, 51, 49, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/44 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290068163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290068163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290068163 none CN(C)CCCC(=O)NC[C@H]1C[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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 30, 22, 13, 13, 13, 11, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 44, 43, 31, 31, 22, 22, 13, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 50, 51, 49, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290068163 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 Building ZINC001290068163 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290068163 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 43) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290068163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290068163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290068163 none CN(C)CCCC(=O)NC[C@H]1C[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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 33, 24, 11, 11, 11, 10, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 44, 44, 33, 33, 24, 24, 11, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 50, 51, 49, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 44) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCC(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290068163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290068163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290068163 none CN(C)CCCC(=O)NC[C@H]1C[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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 30, 22, 13, 13, 13, 11, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 44, 43, 31, 31, 22, 22, 13, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 45, 50, 51, 49, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290068163 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290068163 Building ZINC001290073429 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290073429 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/45 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290073429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290073429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290073429 none Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 31, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/46 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290073429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290073429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290073429 none Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 31, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290073429 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 Building ZINC001290073429 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290073429 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 45) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290073429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290073429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290073429 none Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 31, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 46) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290073429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290073429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290073429 none Cn1c(=O)cccc1C(=O)NC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 31, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290073429 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290073429 Building ZINC001290087776 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290087776 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/47 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1) `ZINC001290087776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290087776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290087776 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 14, 14, 14, 14, 14, 14, 38, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/48 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1) `ZINC001290087776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290087776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290087776 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 17, 17, 17, 17, 17, 17, 41, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 41, 41, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290087776 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 Building ZINC001290087776 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290087776 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 47) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1) `ZINC001290087776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290087776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290087776 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 14, 14, 14, 14, 14, 14, 38, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 48) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1) `ZINC001290087776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290087776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290087776 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 17, 17, 17, 17, 17, 17, 41, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 41, 41, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001290087776 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290087776 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290087776 Building ZINC001290106178 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106178 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/49 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290106178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290106178 none CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 36, 36, 24, 24, 24, 24, 24, 15, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 48, 48, 36, 24, 24, 24, 24, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/50 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290106178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290106178 none CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 48, 29, 29, 29, 20, 20, 20, 20, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 48, 48, 29, 20, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106178 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 Building ZINC001290106178 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106178 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 49) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290106178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290106178 none CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 36, 36, 24, 24, 24, 24, 24, 15, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 48, 48, 36, 24, 24, 24, 24, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 50) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290106178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290106178 none CC(=O)NCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 48, 29, 29, 29, 20, 20, 20, 20, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 48, 48, 29, 20, 20, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106178 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106178 Building ZINC001290106218 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106218 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/51 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/51' -> `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]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1) `ZINC001290106218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106218 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 26, 26, 26, 26, 26, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 26, 26, 26, 26, 36, 50, 50, 50, 50, 26, 26] 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: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/52 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/52' -> `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]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1) `ZINC001290106218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106218 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 22, 22, 22, 22, 22, 22, 31, 31, 31, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 22, 22, 22, 22, 31, 50, 50, 50, 50, 22, 22] 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106218 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 Building ZINC001290106218 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106218 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 51) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1) `ZINC001290106218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106218 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 14, 26, 26, 26, 26, 26, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 13, 13, 26, 26, 26, 26, 36, 50, 50, 50, 50, 26, 26] 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: 184 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 52) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1) `ZINC001290106218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106218 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cc2ncc[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 12, 22, 22, 22, 22, 22, 22, 31, 31, 31, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 22, 22, 22, 22, 31, 50, 50, 50, 50, 22, 22] 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: 183 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106218 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106218 Building ZINC001290106336 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106336 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/53 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/53' -> `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]1CC[C@@H](NC(=O)Cn2cccn2)C1) `ZINC001290106336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106336 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 11, 11, 11, 11, 11, 11, 17, 17, 17, 41, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 17, 41, 41, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/54 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/54' -> `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]1CC[C@@H](NC(=O)Cn2cccn2)C1) `ZINC001290106336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106336 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 12, 12, 12, 12, 12, 21, 21, 21, 45, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 12, 12, 12, 12, 21, 45, 45, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106336 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 Building ZINC001290106336 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106336 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 53) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cccn2)C1) `ZINC001290106336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106336 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 11, 11, 11, 11, 11, 11, 17, 17, 17, 41, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 17, 41, 41, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 54) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cccn2)C1) `ZINC001290106336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290106336 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 12, 12, 12, 12, 12, 21, 21, 21, 45, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 12, 12, 12, 12, 21, 45, 45, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106336 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106336 Building ZINC001290106787 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106787 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/55 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106787 none C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 24, 24, 24, 24, 24, 11, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 37, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/56 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106787 none C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 29, 29, 29, 29, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 37, 29, 29, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106787 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 Building ZINC001290106787 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106787 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 55) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106787 none C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 24, 24, 24, 24, 24, 11, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 37, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 56) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106787 none C[C@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 29, 29, 29, 29, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 37, 29, 29, 29, 29, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106787 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106787 Building ZINC001290106789 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106789 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/57 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106789 none C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 22, 22, 22, 22, 22, 10, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/58 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106789 none C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 49, 38, 38, 25, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 49, 50, 50, 50, 50, 49, 49, 49, 38, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106789 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 Building ZINC001290106789 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290106789 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 57) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290106789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106789 none C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 22, 22, 22, 22, 22, 10, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 58) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1) `ZINC001290106789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290106789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290106789 none C[C@@H](C(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 49, 38, 38, 25, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 49, 50, 50, 50, 50, 49, 49, 49, 38, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290106789 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290106789 Building ZINC001290107173 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107173 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/59 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290107173 none COCCOCC(=O)NC[C@H]1CC[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.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 20, 20, 20, 16, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 47, 47, 42, 42, 20, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/60 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290107173 none COCCOCC(=O)NC[C@H]1CC[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.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 42, 20, 20, 20, 17, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 48, 48, 42, 42, 20, 17, 17, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107173 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 Building ZINC001290107173 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107173 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 59) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290107173 none COCCOCC(=O)NC[C@H]1CC[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.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 20, 20, 20, 16, 8, 8, 8, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 47, 47, 42, 42, 20, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 60) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001290107173 none COCCOCC(=O)NC[C@H]1CC[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.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 42, 20, 20, 20, 17, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 48, 48, 42, 42, 20, 17, 17, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 51, 49, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107173 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107173 Building ZINC001290107190 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107190 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/61 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107190 none CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 23, 23, 17, 17, 17, 17, 17, 11, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 17, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 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: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/62 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107190 none CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 26, 26, 16, 16, 16, 16, 16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 16, 16, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107190 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 Building ZINC001290107190 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107190 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 61) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107190 none CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 23, 23, 17, 17, 17, 17, 17, 11, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 17, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 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: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 62) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290107190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107190 none CN(C)CCC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 26, 26, 16, 16, 16, 16, 16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 16, 16, 16, 16, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107190 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107190 Building ZINC001290107304 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107304 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/63 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/63' -> `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]1CC[C@@H](NC(=O)Cn2cncn2)C1) `ZINC001290107304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290107304 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 41, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 19, 41, 41, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/64 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/64' -> `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]1CC[C@@H](NC(=O)Cn2cncn2)C1) `ZINC001290107304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290107304 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 23, 23, 23, 46, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 13, 13, 13, 13, 23, 46, 46, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107304 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 Building ZINC001290107304 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107304 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 63) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cncn2)C1) `ZINC001290107304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290107304 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 19, 19, 19, 41, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 19, 41, 41, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 64) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cncn2)C1) `ZINC001290107304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290107304 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](NC(=O)Cn2cncn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 23, 23, 23, 46, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 13, 13, 13, 13, 23, 46, 46, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107304 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107304 Building ZINC001290107364 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107364 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/65 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001290107364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107364 none Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 28, 18, 18, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 40, 40, 28, 18, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/66 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001290107364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107364 none Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 28, 20, 20, 20, 20, 20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 42, 42, 28, 20, 20, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50] 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]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107364 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 Building ZINC001290107364 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290107364 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 65) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001290107364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290107364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107364 none Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 28, 18, 18, 18, 18, 18, 8, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 40, 40, 28, 18, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 50] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 66) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001290107364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290107364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290107364 none Cn1cc(CC(=O)N[C@@H]2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 28, 28, 28, 20, 20, 20, 20, 20, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 42, 42, 28, 20, 20, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 50] 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]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290107364 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290107364 Building ZINC001290129540 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290129540 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/67 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290129540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290129540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290129540 none Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 25, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 33, 25, 25, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/68 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290129540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290129540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290129540 none Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 27, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 36, 27, 27, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290129540 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 Building ZINC001290129540 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290129540 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 67) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290129540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290129540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290129540 none Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 25, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 33, 25, 25, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 68) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001290129540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290129540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290129540 none Cn1cnc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 27, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 36, 27, 27, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290129540 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129540 Building ZINC001290129889 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290129889 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/69 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001290129889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290129889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290129889 none Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 49, 35, 16, 16, 16, 16, 16, 5, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 49, 35, 35, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/70 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001290129889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290129889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290129889 none Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 34, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 48, 34, 34, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290129889 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 Building ZINC001290129889 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290129889 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 69) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001290129889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290129889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290129889 none Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 49, 49, 35, 16, 16, 16, 16, 16, 5, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 49, 35, 35, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 70) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001290129889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290129889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290129889 none Cn1cc(C(=O)NC[C@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 48, 48, 34, 14, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 48, 34, 34, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290129889 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290129889 Building ZINC001290188692 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290188692 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/71 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290188692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290188692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290188692 none Cc1nn[nH]c1C(=O)NC[C@H]1CC[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.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 30, 30, 27, 14, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 30, 27, 27, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 147 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/72 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290188692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290188692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290188692 none Cc1nn[nH]c1C(=O)NC[C@H]1CC[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.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 27, 27, 24, 14, 14, 14, 14, 14, 7, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 27, 24, 24, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 136 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290188692 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 Building ZINC001290188692 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290188692 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 71) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290188692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290188692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290188692 none Cc1nn[nH]c1C(=O)NC[C@H]1CC[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.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 30, 30, 27, 14, 14, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 30, 27, 27, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 147 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 72) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn[nH]c1C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290188692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290188692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290188692 none Cc1nn[nH]c1C(=O)NC[C@H]1CC[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.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 27, 27, 27, 24, 14, 14, 14, 14, 14, 7, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 27, 24, 24, 14, 14, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 136 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290188692 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290188692 Building ZINC001290189168 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290189168 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/73 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290189168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189168 none C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 40, 47, 47, 49, 50, 50, 40, 40, 26, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 47, 47, 47, 49, 49, 50, 50, 40, 26, 26, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/74 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290189168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189168 none C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 47, 47, 49, 50, 50, 41, 41, 25, 11, 11, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 47, 47, 47, 49, 49, 50, 50, 41, 25, 25, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290189168 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 Building ZINC001290189168 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290189168 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 73) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290189168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189168 none C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 40, 47, 47, 49, 50, 50, 40, 40, 26, 12, 12, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 47, 47, 47, 49, 49, 50, 50, 40, 26, 26, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 74) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290189168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189168 none C[C@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 47, 47, 49, 50, 50, 41, 41, 25, 11, 11, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 47, 47, 47, 49, 49, 50, 50, 41, 25, 25, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290189168 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189168 Building ZINC001290189169 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290189169 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/75 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290189169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189169 none C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 35, 42, 42, 49, 50, 50, 35, 35, 21, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 49, 49, 50, 50, 35, 21, 21, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/76 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290189169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189169 none C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 42, 48, 48, 50, 50, 50, 42, 42, 27, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 48, 48, 48, 50, 50, 50, 50, 42, 27, 27, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290189169 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 Building ZINC001290189169 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290189169 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 75) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290189169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189169 none C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 35, 42, 42, 49, 50, 50, 35, 35, 21, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 49, 49, 50, 50, 35, 21, 21, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 76) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290189169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290189169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290189169 none C[C@@H](CC(N)=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 42, 48, 48, 50, 50, 50, 42, 42, 27, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 48, 48, 48, 50, 50, 50, 50, 42, 27, 27, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290189169 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290189169 Building ZINC001290276761 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290276761 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/77 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1) `ZINC001290276761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290276761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290276761 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 3, 5, 19, 19, 5, 5, 5, 5, 10] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/78 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1) `ZINC001290276761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290276761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290276761 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 3, 5, 19, 19, 5, 5, 5, 5, 10] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290276761 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 Building ZINC001290276761 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290276761 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 77) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1) `ZINC001290276761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290276761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290276761 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 3, 5, 19, 19, 5, 5, 5, 5, 10] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 78) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1) `ZINC001290276761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290276761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290276761 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 3, 5, 19, 19, 5, 5, 5, 5, 10] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290276761 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290276761 Building ZINC001290291880 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290291880 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/79 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1) `ZINC001290291880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290291880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290291880 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 33, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 50, 2, 2] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/80 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1) `ZINC001290291880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290291880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290291880 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 18, 18, 18, 34, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 18, 34, 34, 50, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290291880 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 Building ZINC001290291880 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290291880 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 79) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1) `ZINC001290291880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290291880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290291880 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 33, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 33, 33, 50, 2, 2] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 80) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1) `ZINC001290291880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290291880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290291880 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 18, 18, 18, 34, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 18, 34, 34, 50, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290291880 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290291880 Building ZINC001290292056 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290292056 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/81 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001290292056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290292056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290292056 none CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 23, 23, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 23, 13, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 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, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/82 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001290292056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290292056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290292056 none CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 25, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 45, 45, 25, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290292056 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 Building ZINC001290292056 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290292056 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 81) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001290292056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290292056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290292056 none CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 23, 23, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 44, 44, 23, 13, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 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, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 194 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 82) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001290292056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290292056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290292056 none CNC(=O)CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 25, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 45, 45, 25, 13, 13, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290292056 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290292056 Building ZINC001290362796 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290362796 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/83 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1) `ZINC001290362796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290362796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290362796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 8, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 25, 28, 28, 28, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 12, 25, 25, 28, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/84 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1) `ZINC001290362796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290362796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290362796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 8, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 22, 25, 25, 25, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 22, 22, 25, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290362796 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 Building ZINC001290362796 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290362796 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 83) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1) `ZINC001290362796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290362796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290362796 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 8, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 25, 28, 28, 28, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 12, 25, 25, 28, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 84) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1) `ZINC001290362796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290362796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290362796 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCc1cc(O)nc(CNC(=O)C2CCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 8, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 22, 25, 25, 25, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 22, 22, 25, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290362796 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290362796 Building ZINC001290404072 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290404072 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/85 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1) `ZINC001290404072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290404072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290404072 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 27, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/86 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1) `ZINC001290404072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290404072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290404072 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 22, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290404072 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 Building ZINC001290404072 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290404072 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 85) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1) `ZINC001290404072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290404072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290404072 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 27, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 27, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 86) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1) `ZINC001290404072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290404072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290404072 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 22, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290404072 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404072 Building ZINC001290404819 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290404819 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/87 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21) `ZINC001290404819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290404819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290404819 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', '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, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/88 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21) `ZINC001290404819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290404819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290404819 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', '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, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290404819 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 Building ZINC001290404819 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290404819 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 87) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21) `ZINC001290404819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290404819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290404819 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', '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, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 88) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21) `ZINC001290404819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290404819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290404819 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', '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, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290404819 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290404819 Building ZINC001290405621 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290405621 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/89 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N) `ZINC001290405621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290405621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290405621 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/90 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N) `ZINC001290405621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290405621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290405621 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290405621 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 Building ZINC001290405621 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290405621 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 89) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N) `ZINC001290405621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290405621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290405621 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 90) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N) `ZINC001290405621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290405621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290405621 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nccnc1N NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290405621 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290405621 Building ZINC001290406036 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290406036 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/91 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C) `ZINC001290406036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290406036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290406036 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/92 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C) `ZINC001290406036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290406036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290406036 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 31, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290406036 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 Building ZINC001290406036 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290406036 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 91) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C) `ZINC001290406036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290406036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290406036 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 92) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C) `ZINC001290406036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290406036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001290406036 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1nnn(C)c1C NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 31, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290406036 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290406036 Building ZINC001290438146 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290438146 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/93 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001290438146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290438146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290438146 none CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 20, 23, 40, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 20, 20, 29, 29, 36, 37, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/94 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001290438146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290438146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290438146 none CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 5, 27, 28, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 27, 27, 38, 38, 46, 45, 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, 6, 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] set([32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 39, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290438146 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 Building ZINC001290438146 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290438146 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 93) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001290438146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290438146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290438146 none CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 20, 23, 40, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 20, 20, 29, 29, 36, 37, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 94) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001290438146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290438146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001290438146 none CC[C@@H]1[C@@H](NC(=O)CCCC(N)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 5, 27, 28, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 27, 27, 38, 38, 46, 45, 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, 6, 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] set([32, 33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 39, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290438146 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290438146 Building ZINC001290446201 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290446201 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/95 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290446201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446201 none C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 27, 40, 40, 40, 50, 50, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 27, 27, 27, 40, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 3, 6, 3, 3, 9, 9, 9, 9] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/96 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290446201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446201 none C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 27, 39, 39, 39, 50, 50, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 27, 27, 27, 39, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 3, 6, 3, 3, 9, 9, 9, 9] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 191 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290446201 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 Building ZINC001290446201 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290446201 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 95) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290446201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446201 none C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 27, 40, 40, 40, 50, 50, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 27, 27, 27, 40, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 3, 6, 3, 3, 9, 9, 9, 9] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 96) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290446201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446201 none C[C@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 27, 39, 39, 39, 50, 50, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 27, 27, 27, 39, 50, 50, 50, 50, 50, 9, 9, 9, 9, 3, 3, 6, 3, 3, 9, 9, 9, 9] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 191 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290446201 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446201 Building ZINC001290446202 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290446202 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/97 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290446202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446202 none C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [28, 10, 28, 28, 40, 40, 40, 50, 50, 10, 10, 10, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 28, 28, 28, 40, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 3, 6, 3, 3, 10, 10, 10, 10] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/98 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290446202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446202 none C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 27, 37, 37, 37, 50, 50, 10, 10, 10, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 27, 27, 27, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 4, 2, 2, 10, 10, 10, 10] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290446202 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 Building ZINC001290446202 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290446202 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 97) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290446202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446202 none C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [28, 10, 28, 28, 40, 40, 40, 50, 50, 10, 10, 10, 4, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 28, 28, 28, 40, 50, 50, 50, 50, 50, 10, 10, 10, 10, 3, 3, 6, 3, 3, 10, 10, 10, 10] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 98) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001290446202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290446202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290446202 none C[C@@H](C(=O)NC1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 27, 37, 37, 37, 50, 50, 10, 10, 10, 4, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 27, 27, 27, 37, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 4, 2, 2, 10, 10, 10, 10] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290446202 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290446202 Building ZINC001290480568 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290480568 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/99 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480568 none COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 38, 17, 12, 17, 12, 12, 12, 12, 4, 12, 2, 4, 6, 10, 1, 2, 1, 1, 1, 1, 1, 1, 12, 45, 45, 45, 38, 38, 12, 12, 12, 12, 12, 12, 6, 6, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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]) total number of confs: 229 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/100 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480568 none COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 11, 16, 11, 11, 11, 11, 4, 11, 2, 4, 7, 11, 1, 2, 1, 1, 1, 1, 1, 1, 11, 44, 44, 44, 37, 37, 11, 11, 11, 11, 11, 11, 7, 7, 11, 11, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 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]) total number of confs: 231 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290480568 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 Building ZINC001290480568 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290480568 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 99) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480568 none COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 38, 17, 12, 17, 12, 12, 12, 12, 4, 12, 2, 4, 6, 10, 1, 2, 1, 1, 1, 1, 1, 1, 12, 45, 45, 45, 38, 38, 12, 12, 12, 12, 12, 12, 6, 6, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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]) total number of confs: 229 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 100) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290480568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480568 none COCC(=O)N1CCC[C@@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 11, 16, 11, 11, 11, 11, 4, 11, 2, 4, 7, 11, 1, 2, 1, 1, 1, 1, 1, 1, 11, 44, 44, 44, 37, 37, 11, 11, 11, 11, 11, 11, 7, 7, 11, 11, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 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]) total number of confs: 231 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290480568 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480568 Building ZINC001290480569 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290480569 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/101 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290480569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480569 none COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 35, 16, 8, 16, 8, 8, 8, 8, 4, 8, 2, 4, 7, 11, 1, 2, 1, 1, 1, 1, 1, 1, 8, 43, 43, 43, 35, 35, 8, 8, 8, 8, 8, 8, 7, 7, 11, 11, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 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]) total number of confs: 232 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/102 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290480569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480569 none COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 9, 18, 9, 9, 9, 9, 3, 9, 2, 3, 4, 7, 1, 2, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 37, 37, 9, 9, 9, 9, 9, 9, 4, 4, 7, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 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]) total number of confs: 194 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290480569 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 Building ZINC001290480569 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290480569 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 101) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290480569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480569 none COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 35, 16, 8, 16, 8, 8, 8, 8, 4, 8, 2, 4, 7, 11, 1, 2, 1, 1, 1, 1, 1, 1, 8, 43, 43, 43, 35, 35, 8, 8, 8, 8, 8, 8, 7, 7, 11, 11, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 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]) total number of confs: 232 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 102) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001290480569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290480569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001290480569 none COCC(=O)N1CCC[C@H](N(CCO)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 5, 12, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 9, 18, 9, 9, 9, 9, 3, 9, 2, 3, 4, 7, 1, 2, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 37, 37, 9, 9, 9, 9, 9, 9, 4, 4, 7, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 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]) total number of confs: 194 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290480569 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290480569 Building ZINC001290597310 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290597310 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/103 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/103' -> `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)c1ccc(=O)n(C)c1) `ZINC001290597310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290597310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290597310 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 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 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/104 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/104' -> `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)c1ccc(=O)n(C)c1) `ZINC001290597310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290597310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290597310 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 25, 25, 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 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290597310 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 Building ZINC001290597310 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290597310 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 103) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)c1) `ZINC001290597310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290597310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290597310 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 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 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 104) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)c1) `ZINC001290597310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290597310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290597310 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 25, 25, 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 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290597310 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597310 Building ZINC001290597932 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290597932 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/105 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1) `ZINC001290597932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290597932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290597932 none Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 12, 10, 12, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 39, 39, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/106 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1) `ZINC001290597932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290597932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290597932 none Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 14, 11, 14, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 43, 43, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290597932 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 Building ZINC001290597932 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290597932 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 105) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1) `ZINC001290597932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290597932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290597932 none Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 12, 10, 12, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 39, 39, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 106) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1) `ZINC001290597932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290597932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290597932 none Cc1cnn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 14, 11, 14, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 43, 43, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290597932 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290597932 Building ZINC001290598209 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598209 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/107 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/107' -> `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)c1cccn(C)c1=O) `ZINC001290598209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598209 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cccn(C)c1=O 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', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 5, 1, 11, 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, 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: [15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/108 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/108' -> `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)c1cccn(C)c1=O) `ZINC001290598209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598209 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cccn(C)c1=O 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', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 5, 1, 11, 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, 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: [15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 37, 37, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598209 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 Building ZINC001290598209 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598209 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 107) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cccn(C)c1=O) `ZINC001290598209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598209 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cccn(C)c1=O 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', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 5, 1, 11, 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, 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: [15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 36, 36, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 108) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cccn(C)c1=O) `ZINC001290598209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598209 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1cccn(C)c1=O 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', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 5, 1, 11, 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, 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: [15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 37, 37, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598209 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598209 Building ZINC001290598552 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598552 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/109 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/109' -> `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]1CCN(C)C1=O) `ZINC001290598552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598552 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 41, 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] 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]) total number of confs: 142 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/110 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/110' -> `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]1CCN(C)C1=O) `ZINC001290598552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598552 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 41, 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] 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]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598552 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 Building ZINC001290598552 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598552 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 109) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCN(C)C1=O) `ZINC001290598552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598552 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 41, 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] 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]) total number of confs: 142 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 110) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCN(C)C1=O) `ZINC001290598552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598552 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 41, 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] 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]) total number of confs: 146 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598552 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598552 Building ZINC001290598555 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598555 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/111 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/111' -> `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]1CCN(C)C1=O) `ZINC001290598555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598555 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 34, 37, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 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, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/112 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/112' -> `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]1CCN(C)C1=O) `ZINC001290598555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598555 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 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, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598555 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 Building ZINC001290598555 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598555 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 111) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCN(C)C1=O) `ZINC001290598555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598555 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 34, 37, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 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, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 112) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCN(C)C1=O) `ZINC001290598555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290598555 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCN(C)C1=O 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', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 32, 34, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 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, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598555 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598555 Building ZINC001290598861 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598861 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/113 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290598861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290598861 none CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 36, 22, 13, 22, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 50, 50, 50, 50, 50, 36, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/114 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290598861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290598861 none CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 23, 15, 23, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 33, 50, 50, 50, 50, 50, 33, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598861 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 Building ZINC001290598861 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290598861 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 113) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290598861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290598861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290598861 none CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 36, 22, 13, 22, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 50, 50, 50, 50, 50, 36, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 114) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290598861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290598861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290598861 none CCn1ncc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 23, 15, 23, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 33, 50, 50, 50, 50, 50, 33, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290598861 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290598861 Building ZINC001290599252 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290599252 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/115 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001290599252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290599252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290599252 none Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 6, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 14, 11, 14, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 44, 44, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/116 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001290599252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290599252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290599252 none Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 6, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 19, 11, 19, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 46, 46, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290599252 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 Building ZINC001290599252 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290599252 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 115) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001290599252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290599252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290599252 none Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 6, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 14, 11, 14, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 44, 44, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 116) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001290599252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290599252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001290599252 none Cc1nc[nH]c1CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 6, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 19, 11, 19, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 46, 46, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290599252 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599252 Building ZINC001290599994 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290599994 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/117 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C) `ZINC001290599994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290599994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001290599994 none Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 10, 15, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 38, 38, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/118 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C) `ZINC001290599994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290599994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001290599994 none Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 12, 18, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 37, 37, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 156 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290599994 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 Building ZINC001290599994 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290599994 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 117) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C) `ZINC001290599994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290599994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001290599994 none Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 10, 15, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 38, 38, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 118) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C) `ZINC001290599994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290599994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001290599994 none Cc1c(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 12, 18, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 37, 37, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 156 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290599994 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290599994 Building ZINC001290600043 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600043 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/119 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/119' -> `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)CCCCC(N)=O) `ZINC001290600043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600043 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCC(N)=O 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.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'] 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, 5, 1, 8, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 24, 26, 30, 42, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 30, 30, 30, 30, 42, 42, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/120 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/120' -> `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)CCCCC(N)=O) `ZINC001290600043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600043 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCC(N)=O 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.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'] 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, 5, 1, 8, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 9, 22, 24, 27, 43, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 22, 27, 27, 27, 27, 43, 43, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600043 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 Building ZINC001290600043 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600043 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 119) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCC(N)=O) `ZINC001290600043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600043 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCC(N)=O 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.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'] 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, 5, 1, 8, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 9, 9, 24, 26, 30, 42, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 30, 30, 30, 30, 42, 42, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 120) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCC(N)=O) `ZINC001290600043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600043 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCCC(N)=O 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.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'] 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, 5, 1, 8, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 9, 22, 24, 27, 43, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 22, 27, 27, 27, 27, 43, 43, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600043 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600043 Building ZINC001290600341 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600341 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/121 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/121' -> `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)c1ccc(=O)n(C)n1) `ZINC001290600341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290600341 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)n1 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', 'C.2', 'C.2', 'O.2', 'N.am', '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'] 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, 1, 1, 11, 8, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/122 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/122' -> `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)c1ccc(=O)n(C)n1) `ZINC001290600341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290600341 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)n1 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', 'C.2', 'C.2', 'O.2', 'N.am', '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'] 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, 1, 1, 11, 8, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 31, 31, 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 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600341 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 Building ZINC001290600341 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600341 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 121) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)n1) `ZINC001290600341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290600341 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)n1 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', 'C.2', 'C.2', 'O.2', 'N.am', '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'] 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, 1, 1, 11, 8, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 122) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)n1) `ZINC001290600341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290600341 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)c1ccc(=O)n(C)n1 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', 'C.2', 'C.2', 'O.2', 'N.am', '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'] 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, 1, 1, 11, 8, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 31, 31, 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 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600341 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600341 Building ZINC001290600388 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600388 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/123 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/123' -> `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[C@H]1CCNC1=O) `ZINC001290600388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600388 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 47, 50, 50, 50, 50, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 44, 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]) total number of confs: 179 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/124 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/124' -> `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[C@H]1CCNC1=O) `ZINC001290600388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600388 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 24, 24, 49, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 48, 48, 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]) total number of confs: 195 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600388 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 Building ZINC001290600388 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600388 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 123) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@H]1CCNC1=O) `ZINC001290600388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600388 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 47, 50, 50, 50, 50, 50, 50, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 44, 44, 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]) total number of confs: 179 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 124) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@H]1CCNC1=O) `ZINC001290600388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600388 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 24, 24, 49, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 48, 48, 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]) total number of confs: 195 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600388 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600388 Building ZINC001290600389 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600389 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/125 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/125' -> `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[C@@H]1CCNC1=O) `ZINC001290600389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600389 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 20, 20, 49, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 48, 48, 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/126 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/126' -> `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[C@@H]1CCNC1=O) `ZINC001290600389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600389 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 20, 20, 48, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 47, 47, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600389 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 Building ZINC001290600389 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600389 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 125) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@@H]1CCNC1=O) `ZINC001290600389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600389 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 20, 20, 49, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 48, 48, 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 126) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@@H]1CCNC1=O) `ZINC001290600389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001290600389 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C[C@@H]1CCNC1=O 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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 20, 20, 48, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 47, 47, 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600389 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600389 Building ZINC001290600444 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600444 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/127 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290600444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290600444 none Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 11, 8, 11, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 39, 39, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/128 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290600444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290600444 none Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 16, 12, 16, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 50, 43, 43, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600444 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 Building ZINC001290600444 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600444 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 127) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290600444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290600444 none Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 11, 8, 11, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 39, 39, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 128) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1) `ZINC001290600444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290600444 none Cc1ccn(CC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 16, 12, 16, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 50, 43, 43, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600444 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600444 Building ZINC001290600671 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600671 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/129 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/129' -> `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(=O)NCC(F)F) `ZINC001290600671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290600671 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC(F)F 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', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 36, 36, 36, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 36, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/130 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/130' -> `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(=O)NCC(F)F) `ZINC001290600671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290600671 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC(F)F 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', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 34, 34, 34, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 34, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 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/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600671 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 Building ZINC001290600671 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290600671 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 129) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC(F)F) `ZINC001290600671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290600671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290600671 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC(F)F 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', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 36, 36, 36, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 36, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 130) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC(F)F) `ZINC001290600671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290600671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290600671 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)C(=O)NCC(F)F 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', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 34, 34, 34, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 34, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 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, 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/13323/xbn-8058097.40/working/building/ZINC001290600671 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290600671 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290600671 Building ZINC001290665111 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290665111 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/131 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCS(C)(=O)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001290665111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290665111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290665111 none C[C@@H]1[C@@H](NC(=O)CCS(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', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need 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, 13, 13, 13, 39, 44, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 39, 39, 44, 44, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/132 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCS(C)(=O)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001290665111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290665111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290665111 none C[C@@H]1[C@@H](NC(=O)CCS(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', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need 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, 15, 15, 15, 35, 38, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 35, 35, 38, 38, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290665111 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 Building ZINC001290665111 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290665111 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 131) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCS(C)(=O)=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001290665111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290665111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290665111 none C[C@@H]1[C@@H](NC(=O)CCS(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', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need 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, 13, 13, 13, 39, 44, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 39, 39, 44, 44, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 132) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCS(C)(=O)=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001290665111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290665111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001290665111 none C[C@@H]1[C@@H](NC(=O)CCS(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', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need 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, 15, 15, 15, 35, 38, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 35, 35, 38, 38, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290665111 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290665111 Building ZINC001290677522 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290677522 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/133 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001290677522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290677522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001290677522 none CC(=O)NC(C)(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 19, 46, 46, 19, 19, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/134 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001290677522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290677522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001290677522 none CC(=O)NC(C)(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 44, 44, 19, 19, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 19, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290677522 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 Building ZINC001290677522 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290677522 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 133) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001290677522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290677522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001290677522 none CC(=O)NC(C)(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 19, 46, 46, 19, 19, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 134) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001290677522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290677522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001290677522 none CC(=O)NC(C)(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 44, 44, 19, 19, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 19, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290677522 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290677522 Building ZINC001290704742 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290704742 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/135 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001290704742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290704742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001290704742 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 6, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 4, 15, 15, 4, 4, 4, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/136 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001290704742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290704742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001290704742 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 7, 10, 10, 7, 10, 10, 8, 8, 8, 8, 8, 4, 15, 15, 4, 4, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290704742 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 Building ZINC001290704742 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290704742 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 135) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001290704742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290704742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001290704742 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 6, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 4, 15, 15, 4, 4, 4, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 136) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1) `ZINC001290704742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290704742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001290704742 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccccc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 7, 10, 10, 7, 10, 10, 8, 8, 8, 8, 8, 4, 15, 15, 4, 4, 4, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290704742 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290704742 Building ZINC001290774351 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774351 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/137 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774351 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 39, 16, 39, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/138 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774351 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 35, 16, 35, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774351 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 Building ZINC001290774351 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774351 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 137) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774351 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 39, 16, 39, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 138) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774351 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 35, 16, 35, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774351 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774351 Building ZINC001290774352 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774352 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/139 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774352 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 36, 19, 36, 19, 19, 19, 7, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 19, 19] 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]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/140 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774352 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 32, 17, 32, 17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17] 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]) total number of confs: 173 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774352 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 Building ZINC001290774352 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774352 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 139) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774352 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 36, 19, 36, 19, 19, 19, 7, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 19, 19] 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]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 140) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774352 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 32, 17, 32, 17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17] 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]) total number of confs: 173 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774352 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774352 Building ZINC001290774353 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774353 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/141 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774353 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 31, 13, 31, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 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]) total number of confs: 161 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/142 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774353 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 34, 15, 34, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 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]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774353 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 Building ZINC001290774353 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774353 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 141) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774353 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 31, 13, 31, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 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]) total number of confs: 161 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 142) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290774353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774353 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 34, 15, 34, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 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]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774353 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774353 Building ZINC001290774354 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774354 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/143 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774354 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 34, 15, 34, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 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]) total number of confs: 172 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/144 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774354 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 33, 14, 33, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 165 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774354 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 Building ZINC001290774354 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290774354 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 143) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290774354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774354 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 34, 15, 34, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 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]) total number of confs: 172 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 144) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1occc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290774354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290774354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290774354 none Cc1occc1C(=O)N1CC[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.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 12, 1, 1, 1, 1, 11, 8, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 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, 33, 14, 33, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 165 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290774354 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290774354 Building ZINC001290775203 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775203 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/145 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775203 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 150 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 50, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/146 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775203 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 29, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 29, 29, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775203 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 Building ZINC001290775203 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775203 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 145) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775203 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 19, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 150 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 50, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 146) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775203 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 29, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 29, 29, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775203 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775203 Building ZINC001290775204 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775204 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/147 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775204 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 27, 27, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/148 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775204 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 150 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 50, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775204 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 Building ZINC001290775204 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775204 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 147) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775204 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 6, 6, 6, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 27, 27, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 148) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775204 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 150 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 50, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775204 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775204 Building ZINC001290775205 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775205 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/149 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775205 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 28, 6, 6, 6, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 28, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/150 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775205 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 35, 12, 12, 12, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 35, 35, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775205 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 Building ZINC001290775205 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775205 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 149) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775205 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 28, 6, 6, 6, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 28, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 150) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290775205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775205 none CCCSCC(=O)N[C@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 35, 12, 12, 12, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 35, 35, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775205 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775205 Building ZINC001290775206 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775206 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/151 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775206 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 32, 9, 9, 9, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 32, 32, 9, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/152 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775206 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 6, 6, 6, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 27, 27, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775206 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 Building ZINC001290775206 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775206 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 151) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775206 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 32, 9, 9, 9, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 32, 32, 9, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 152) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290775206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290775206 none CCCSCC(=O)N[C@@H]1CCN(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', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [5, 5, 5, 14, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 27, 6, 6, 6, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 27, 27, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775206 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775206 Building ZINC001290775616 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775616 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/153 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775616 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 10, 10, 10, 10, 10, 20, 20, 38, 48, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 38, 38, 50, 50, 50, 10, 10, 30] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 245 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/154 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775616 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 9, 9, 9, 9, 9, 16, 16, 31, 49, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 31, 31, 50, 50, 50, 9, 9, 27] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775616 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 Building ZINC001290775616 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775616 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 153) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775616 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 10, 10, 10, 10, 10, 20, 20, 38, 48, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 38, 38, 50, 50, 50, 10, 10, 30] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 245 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 154) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775616 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 9, 9, 9, 9, 9, 16, 16, 31, 49, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 31, 31, 50, 50, 50, 9, 9, 27] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 251 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775616 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775616 Building ZINC001290775617 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775617 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/155 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775617 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 13, 13, 13, 13, 13, 22, 22, 35, 49, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 35, 35, 50, 50, 50, 13, 13, 39] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 259 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/156 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775617 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 12, 12, 12, 12, 12, 22, 22, 35, 49, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 35, 35, 50, 50, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 257 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775617 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 Building ZINC001290775617 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775617 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 155) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775617 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 13, 13, 13, 13, 13, 22, 22, 35, 49, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 35, 35, 50, 50, 50, 13, 13, 39] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 259 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 156) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775617 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 12, 12, 12, 12, 12, 22, 22, 35, 49, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 35, 35, 50, 50, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 257 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775617 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775617 Building ZINC001290775618 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775618 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/157 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775618 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 8, 19, 19, 34, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 34, 34, 50, 50, 50, 8, 8, 24] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/158 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775618 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 3, 8, 8, 8, 8, 8, 18, 18, 30, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 30, 30, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775618 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 Building ZINC001290775618 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775618 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 157) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775618 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 8, 19, 19, 34, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 34, 34, 50, 50, 50, 8, 8, 24] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 225 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 158) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)C[C@H]1O) `ZINC001290775618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775618 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 3, 8, 8, 8, 8, 8, 18, 18, 30, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 30, 30, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 229 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775618 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775618 Building ZINC001290775619 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775619 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/159 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775619 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 2, 7, 7, 7, 7, 7, 18, 18, 33, 49, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 33, 33, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/160 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775619 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 6, 6, 6, 6, 6, 17, 17, 34, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 34, 34, 50, 50, 50, 6, 6, 18] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 227 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775619 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 Building ZINC001290775619 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775619 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 159) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775619 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 2, 7, 7, 7, 7, 7, 18, 18, 33, 49, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 33, 33, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 160) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)C[C@@H]1O) `ZINC001290775619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775619 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CC(C)(F)F)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 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] 1 hydrogens 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, 6, 6, 6, 6, 6, 17, 17, 34, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 34, 34, 50, 50, 50, 6, 6, 18] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 227 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775619 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775619 Building ZINC001290775800 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775800 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/161 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775800 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 17, 38, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/162 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775800 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 17, 36, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775800 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 Building ZINC001290775800 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775800 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 161) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775800 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 17, 38, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 162) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775800 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 17, 36, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775800 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775800 Building ZINC001290775807 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775807 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/163 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775807 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 16, 36, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16, 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]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/164 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775807 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 37, 15, 37, 15, 15, 15, 3, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775807 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 Building ZINC001290775807 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775807 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 163) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775807 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 16, 36, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16, 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]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 164) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775807 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 37, 15, 37, 15, 15, 15, 3, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775807 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775807 Building ZINC001290775809 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775809 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/165 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775809 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 12, 38, 12, 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, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 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]) total number of confs: 160 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/166 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775809 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 10, 33, 10, 10, 10, 5, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775809 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 Building ZINC001290775809 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775809 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 165) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775809 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 12, 38, 12, 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, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 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]) total number of confs: 160 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 166) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290775809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775809 none Cc1cnc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 10, 33, 10, 10, 10, 5, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775809 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775809 Building ZINC001290775811 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775811 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/167 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775811 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 35, 11, 35, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/168 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775811 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 39, 15, 39, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 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]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775811 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 Building ZINC001290775811 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775811 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 167) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775811 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 35, 11, 35, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 168) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290775811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290775811 none Cc1cnc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 3, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 39, 15, 39, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 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]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775811 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775811 Building ZINC001290775990 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775990 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/169 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775990 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 7, 17, 17, 17, 17, 17, 44, 44, 48, 50, 50, 48, 48, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 48, 48, 48, 48, 17, 17, 51] 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, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/170 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775990 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 17, 45, 45, 48, 50, 50, 48, 48, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 48, 48, 48, 48, 17, 17, 51] 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, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775990 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 Building ZINC001290775990 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775990 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 169) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775990 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 7, 17, 17, 17, 17, 17, 44, 44, 48, 50, 50, 48, 48, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 48, 48, 48, 48, 17, 17, 51] 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, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 170) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775990 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 6, 17, 17, 17, 17, 17, 45, 45, 48, 50, 50, 48, 48, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 48, 48, 48, 48, 17, 17, 51] 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, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775990 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775990 Building ZINC001290775996 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775996 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/171 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775996 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 6, 23, 23, 23, 23, 23, 46, 46, 47, 50, 50, 47, 47, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 47, 47, 47, 47, 23, 23, 69] 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, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/172 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775996 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 8, 22, 22, 22, 22, 22, 44, 44, 47, 50, 50, 47, 47, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 50, 47, 47, 47, 47, 22, 22, 66] 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, 48, 49, 50]) total number of confs: 211 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775996 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 Building ZINC001290775996 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775996 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 171) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775996 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 6, 23, 23, 23, 23, 23, 46, 46, 47, 50, 50, 47, 47, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 47, 47, 47, 47, 23, 23, 69] 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, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 172) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775996 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 8, 22, 22, 22, 22, 22, 44, 44, 47, 50, 50, 47, 47, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 50, 47, 47, 47, 47, 22, 22, 66] 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, 48, 49, 50]) total number of confs: 211 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775996 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775996 Building ZINC001290775998 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775998 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/173 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775998 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 19, 19, 19, 19, 19, 39, 39, 49, 50, 50, 49, 49, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 50, 49, 49, 49, 49, 19, 19, 57] 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, 48, 49, 50]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/174 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775998 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 21, 21, 21, 21, 21, 39, 39, 49, 50, 50, 49, 49, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 21, 50, 50, 50, 50, 49, 49, 49, 49, 21, 21, 63] 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, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775998 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 Building ZINC001290775998 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775998 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 173) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775998 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 19, 19, 19, 19, 19, 39, 39, 49, 50, 50, 49, 49, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 50, 49, 49, 49, 49, 19, 19, 57] 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, 48, 49, 50]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 174) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)CC2)C[C@@H]1O) `ZINC001290775998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775998 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 21, 21, 21, 21, 21, 39, 39, 49, 50, 50, 49, 49, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 21, 50, 50, 50, 50, 49, 49, 49, 49, 21, 21, 63] 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, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775998 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775998 Building ZINC001290775999 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775999 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/175 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775999 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 18, 39, 39, 49, 50, 50, 49, 49, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 49, 49, 49, 49, 18, 18, 54] 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, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/176 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775999 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 16, 16, 16, 16, 16, 40, 40, 48, 50, 50, 48, 48, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 48, 48, 48, 48, 16, 16, 48] 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, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775999 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 Building ZINC001290775999 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290775999 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 175) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290775999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775999 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 18, 39, 39, 49, 50, 50, 49, 49, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 49, 49, 49, 49, 18, 18, 54] 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, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 176) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)CC2)C[C@H]1O) `ZINC001290775999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290775999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290775999 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(CCF)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 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, 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, 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, 7, 7] 1 hydrogens 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, 16, 16, 16, 16, 16, 40, 40, 48, 50, 50, 48, 48, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 48, 48, 48, 48, 16, 16, 48] 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, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290775999 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290775999 Building ZINC001290776346 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776346 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/177 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776346 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 44, 29, 6, 6, 6, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 44, 44, 29, 29, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/178 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776346 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 48, 41, 8, 8, 8, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 41, 41, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776346 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 Building ZINC001290776346 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776346 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 177) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776346 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 44, 29, 6, 6, 6, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 44, 44, 29, 29, 6, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 178) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776346 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 48, 41, 8, 8, 8, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 41, 41, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 202 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776346 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776346 Building ZINC001290776348 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776348 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/179 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776348 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 47, 41, 8, 8, 8, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 47, 47, 41, 41, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/180 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776348 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 42, 26, 5, 5, 5, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 42, 42, 26, 26, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 12, 13, 46, 15, 16, 17, 18, 19, 20, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776348 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 Building ZINC001290776348 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776348 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 179) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776348 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 47, 41, 8, 8, 8, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 47, 47, 41, 41, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 180) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776348 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 42, 26, 5, 5, 5, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 42, 42, 26, 26, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 12, 13, 46, 15, 16, 17, 18, 19, 20, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776348 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776348 Building ZINC001290776350 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776350 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/181 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776350 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 48, 37, 10, 10, 10, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 48, 48, 37, 37, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/182 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776350 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 41, 13, 13, 13, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 41, 41, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 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/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776350 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 Building ZINC001290776350 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776350 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 181) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776350 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 48, 37, 10, 10, 10, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 48, 48, 37, 37, 10, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 182) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001290776350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776350 none CCOCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 41, 13, 13, 13, 8, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 41, 41, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 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/13323/xbn-8058097.40/working/building/ZINC001290776350 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776350 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776350 Building ZINC001290776352 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776352 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/183 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776352 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 16, 16, 16, 11, 11, 11, 11, 11, 11, 2, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 16, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/184 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776352 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 48, 37, 10, 10, 10, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 37, 37, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 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/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776352 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 Building ZINC001290776352 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290776352 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 183) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290776352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776352 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 16, 16, 16, 11, 11, 11, 11, 11, 11, 2, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 40, 40, 16, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 49, 50]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 184) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001290776352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290776352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290776352 none CCOCCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O 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', 'C.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: [5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 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, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 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, 48, 37, 10, 10, 10, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 37, 37, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] 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, 48, 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/13323/xbn-8058097.40/working/building/ZINC001290776352 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290776352 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290776352 Building ZINC001290777508 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777508 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/185 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777508 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 17, 29, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/186 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777508 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 12, 28, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777508 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 Building ZINC001290777508 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777508 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 185) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777508 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 17, 29, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 186) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777508 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 12, 28, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777508 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777508 Building ZINC001290777509 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777509 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/187 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777509 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 13, 33, 13, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/188 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777509 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 15, 32, 15, 15, 15, 3, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777509 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 Building ZINC001290777509 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777509 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 187) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777509 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 13, 33, 13, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 188) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001290777509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777509 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 15, 32, 15, 15, 15, 3, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777509 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777509 Building ZINC001290777510 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777510 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/189 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777510 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 14, 31, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/190 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777510 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 12, 28, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777510 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 Building ZINC001290777510 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777510 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 189) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777510 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 14, 31, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 190) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777510 none Cc1ccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 12, 28, 12, 12, 12, 5, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777510 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777510 Building ZINC001290777511 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777511 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/191 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777511 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 3, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/192 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777511 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 37, 17, 37, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777511 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 Building ZINC001290777511 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777511 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 191) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777511 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 3, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 192) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1) `ZINC001290777511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001290777511 none Cc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 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, 7, 7, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 37, 17, 37, 17, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 50] 150 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777511 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777511 Building ZINC001290777568 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777568 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/193 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777568 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 37, 15, 37, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 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]) total number of confs: 171 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/194 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777568 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 36, 17, 36, 17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17] 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]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777568 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 Building ZINC001290777568 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777568 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 193) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777568 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 37, 15, 37, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 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]) total number of confs: 171 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 194) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777568 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 36, 17, 36, 17, 17, 17, 5, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17] 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]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777568 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777568 Building ZINC001290777569 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777569 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/195 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777569 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 37, 12, 37, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 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]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/196 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777569 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 32, 13, 32, 13, 13, 13, 5, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 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]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777569 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 Building ZINC001290777569 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777569 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 195) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777569 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 37, 12, 37, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 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]) total number of confs: 160 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 196) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777569 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 32, 13, 32, 13, 13, 13, 5, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 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]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777569 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777569 Building ZINC001290777570 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777570 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/197 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777570 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 33, 14, 33, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/198 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777570 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 35, 14, 35, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777570 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 Building ZINC001290777570 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777570 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 197) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777570 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 33, 14, 33, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 198) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290777570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777570 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 35, 14, 35, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777570 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777570 Building ZINC001290777571 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777571 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/199 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777571 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 39, 12, 39, 12, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 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]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/200 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777571 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 34, 14, 34, 14, 14, 14, 3, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777571 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 Building ZINC001290777571 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290777571 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 199) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290777571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777571 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 39, 12, 39, 12, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 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]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 200) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nocc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290777571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290777571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001290777571 none Cc1nocc1C(=O)N1CC[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', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 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, 3, 7, 7, 7, 6, 7, 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] 1 hydrogens need rotated 150 conformations 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, 34, 14, 34, 14, 14, 14, 3, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290777571 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290777571 Building ZINC001290778476 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778476 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/201 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778476 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 37, 14, 37, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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: 160 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/202 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778476 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 37, 14, 37, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778476 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 Building ZINC001290778476 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778476 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 201) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778476 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 37, 14, 37, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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: 160 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 202) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778476 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 37, 14, 37, 14, 14, 14, 5, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778476 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778476 Building ZINC001290778477 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778477 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/203 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778477 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 39, 19, 39, 19, 19, 19, 3, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 19, 19] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/204 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778477 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 34, 16, 34, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778477 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 Building ZINC001290778477 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778477 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 203) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778477 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 39, 19, 39, 19, 19, 19, 3, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 19, 19] 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: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 204) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778477 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 34, 16, 34, 16, 16, 16, 3, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778477 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778477 Building ZINC001290778478 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778478 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/205 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778478 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 6, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/206 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778478 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 37, 16, 37, 16, 16, 16, 5, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778478 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 Building ZINC001290778478 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778478 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 205) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778478 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 35, 14, 35, 14, 14, 14, 6, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 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: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 206) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001290778478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778478 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 37, 16, 37, 16, 16, 16, 5, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 16, 16] 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: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778478 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778478 Building ZINC001290778479 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778479 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/207 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778479 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 30, 13, 30, 13, 13, 13, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 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, 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: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/208 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778479 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 36, 15, 36, 15, 15, 15, 3, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 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: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778479 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 Building ZINC001290778479 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778479 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 207) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778479 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 30, 13, 30, 13, 13, 13, 2, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 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, 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: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 208) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)n1) `ZINC001290778479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290778479 none Cc1cccc(C(=O)N2CC[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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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, 50, 50, 50, 50, 36, 15, 36, 15, 15, 15, 3, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 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: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778479 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778479 Building ZINC001290778632 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778632 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/209 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778632 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 32, 31, 19, 8, 19, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 49, 49, 34, 34, 31, 31, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 236 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/210 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778632 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 30, 27, 14, 6, 14, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 48, 48, 34, 34, 27, 27, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 249 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778632 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 Building ZINC001290778632 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778632 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 209) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778632 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 32, 31, 19, 8, 19, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 49, 49, 34, 34, 31, 31, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 236 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 210) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778632 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 30, 27, 14, 6, 14, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 48, 48, 34, 34, 27, 27, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 249 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778632 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778632 Building ZINC001290778634 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778634 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/211 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778634 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 30, 27, 14, 6, 14, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 48, 48, 34, 34, 27, 27, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 247 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/212 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778634 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 30, 29, 18, 8, 18, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 49, 49, 32, 32, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778634 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 Building ZINC001290778634 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778634 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 211) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778634 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 30, 27, 14, 6, 14, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 48, 48, 34, 34, 27, 27, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 247 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 212) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778634 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 30, 29, 18, 8, 18, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 49, 49, 32, 32, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778634 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778634 Building ZINC001290778635 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778635 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/213 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778635 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 25, 18, 9, 7, 9, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 49, 50, 26, 26, 18, 18, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/214 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778635 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 26, 22, 11, 7, 11, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 49, 50, 28, 28, 22, 22, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 253 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778635 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 Building ZINC001290778635 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778635 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 213) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778635 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 25, 18, 9, 7, 9, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 49, 50, 26, 26, 18, 18, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 214) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290778635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778635 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 26, 22, 11, 7, 11, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 49, 50, 28, 28, 22, 22, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 253 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778635 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778635 Building ZINC001290778637 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778637 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/215 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778637 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 26, 22, 12, 9, 12, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 49, 28, 28, 22, 22, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 256 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/216 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778637 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 26, 20, 9, 7, 9, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 48, 28, 28, 20, 20, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778637 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 Building ZINC001290778637 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290778637 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 215) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290778637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778637 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 26, 22, 12, 9, 12, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 49, 28, 28, 22, 22, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 256 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 216) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290778637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290778637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290778637 none COCCCC(=O)N1CC[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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 12, 5, 5, 5, 1, 11, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 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, 26, 20, 9, 7, 9, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 48, 28, 28, 20, 20, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290778637 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290778637 Building ZINC001290779435 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779435 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/217 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779435 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 16, 16, 16, 16, 16, 39, 46, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 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, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/218 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779435 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 17, 17, 17, 17, 17, 39, 47, 50, 50, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 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, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779435 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 Building ZINC001290779435 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779435 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 217) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779435 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 16, 16, 16, 16, 16, 39, 46, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 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, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 218) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779435 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 17, 17, 17, 17, 17, 39, 47, 50, 50, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 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, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779435 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779435 Building ZINC001290779436 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779436 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/219 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779436 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 22, 24, 24, 24, 24, 42, 48, 50, 50, 50, 50, 50, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 72] 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, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/220 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779436 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 25, 27, 27, 27, 27, 42, 47, 50, 50, 50, 50, 50, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 81] 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, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779436 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 Building ZINC001290779436 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779436 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 219) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779436 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 22, 24, 24, 24, 24, 42, 48, 50, 50, 50, 50, 50, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 72] 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, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 220) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779436 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 25, 27, 27, 27, 27, 42, 47, 50, 50, 50, 50, 50, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 81] 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, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779436 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779436 Building ZINC001290779438 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779438 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/221 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779438 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 22, 22, 22, 22, 42, 47, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 66] 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, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/222 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779438 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 23, 23, 23, 23, 42, 48, 50, 50, 50, 50, 50, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 69] 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, 48, 49, 50]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779438 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 Building ZINC001290779438 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779438 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 221) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779438 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 22, 22, 22, 22, 42, 47, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 66] 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, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 222) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)C[C@@H]1O) `ZINC001290779438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779438 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 23, 23, 23, 23, 42, 48, 50, 50, 50, 50, 50, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 69] 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, 48, 49, 50]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779438 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779438 Building ZINC001290779439 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779439 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/223 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779439 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 18, 18, 18, 18, 38, 48, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 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, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/224 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779439 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 18, 18, 18, 18, 35, 46, 50, 50, 50, 50, 50, 18, 17, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 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, 48, 49, 50]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779439 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 Building ZINC001290779439 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779439 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 223) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779439.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779439 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 18, 18, 18, 18, 38, 48, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 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, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 224) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)C[C@H]1O) `ZINC001290779439.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290779439 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2(F)CCCC2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 18, 18, 18, 18, 35, 46, 50, 50, 50, 50, 50, 18, 17, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 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, 48, 49, 50]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779439 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779439 Building ZINC001290780020 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780020 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/225 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/226 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/227 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/227' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/228 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/228' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780020 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 Building ZINC001290780020 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780020 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 225) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 226) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 227) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 228) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780020 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 Building ZINC001290780020 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780020 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 225) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 226) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 227) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 228) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780020 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 Building ZINC001290780020 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780020 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 225) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 226) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 23, 15, 23, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 227) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 228) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780020.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780020 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 14, 20, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780020 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780020 Building ZINC001290779978 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779978 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/229 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779978 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 12, 27, 12, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 44, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/230 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779978 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 12, 30, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779978 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 Building ZINC001290779978 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779978 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 229) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779978 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 12, 27, 12, 12, 12, 2, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 44, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 230) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779978 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 12, 30, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 153 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779978 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779978 Building ZINC001290779979 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779979 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/231 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779979 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 13, 31, 13, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 31, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/232 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779979 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 15, 30, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 48, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779979 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 Building ZINC001290779979 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779979 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 231) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779979 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 13, 31, 13, 13, 13, 6, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 31, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 232) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1) `ZINC001290779979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779979 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 15, 30, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 48, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779979 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779979 Building ZINC001290779981 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779981 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/233 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779981 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 11, 31, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 48, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/234 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779981 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 11, 29, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 47, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779981 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 Building ZINC001290779981 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779981 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 233) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779981 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 11, 31, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 48, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 234) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779981 none Cc1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 11, 29, 11, 11, 11, 5, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 47, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779981 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779981 Building ZINC001290779983 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779983 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/235 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779983 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 11, 30, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/236 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779983 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 13, 32, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779983 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 Building ZINC001290779983 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290779983 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 235) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290779983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779983 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 11, 30, 11, 11, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 236) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1) `ZINC001290779983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290779983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001290779983 none Cc1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C2)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 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, 13, 32, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290779983 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290779983 Building ZINC001290780007 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780007 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/237 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780007 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 11, 11, 11, 11, 11, 24, 37, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/238 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780007 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 10, 10, 10, 10, 10, 21, 32, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 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: 173 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780007 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 Building ZINC001290780007 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780007 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 237) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780007 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 11, 11, 11, 11, 11, 24, 37, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 238) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780007 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 10, 10, 10, 10, 10, 21, 32, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 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: 173 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780007 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780007 Building ZINC001290780009 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780009 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/239 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780009 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 10, 10, 25, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 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: 166 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/240 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780009 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 22, 34, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780009 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 Building ZINC001290780009 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780009 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 239) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780009 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 10, 10, 25, 36, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 30] 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: 166 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 240) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780009 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 22, 34, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 170 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780009 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780009 Building ZINC001290780011 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780011 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/241 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780011 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 13, 13, 13, 13, 13, 24, 37, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 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: 171 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/242 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780011 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 13, 13, 13, 13, 13, 24, 36, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 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: 172 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780011 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 Building ZINC001290780011 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780011 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 241) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780011 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 13, 13, 13, 13, 13, 24, 37, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 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: 171 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 242) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@@H]1O) `ZINC001290780011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780011 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 13, 13, 13, 13, 13, 24, 36, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 39] 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: 172 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780011 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780011 Building ZINC001290780013 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780013 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/243 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780013 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 12, 12, 12, 12, 12, 22, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/244 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780013 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 12, 12, 28, 37, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780013 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 Building ZINC001290780013 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290780013 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 243) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780013 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 12, 12, 12, 12, 12, 22, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 244) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(F)(F)C2)C[C@H]1O) `ZINC001290780013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001290780013 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)C2CC(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 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, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 12, 12, 28, 37, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 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, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780013 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780013 Building ZINC001290780014 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780014 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/245 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/246 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/247 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/247' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/248 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/248' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780014 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 Building ZINC001290780014 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780014 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 245) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 246) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 247) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 248) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780014 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 Building ZINC001290780014 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780014 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 245) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 246) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 247) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 248) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780014 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 Building ZINC001290780014 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780014 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 245) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 246) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 20, 10, 20, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 247) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 248) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780014.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780014 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 18, 10, 18, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 214 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780014 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780014 Building ZINC001290780016 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780016 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/249 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/250 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/251 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/251' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/252 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/252' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780016 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 Building ZINC001290780016 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780016 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 249) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 250) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 251) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 252) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780016 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 Building ZINC001290780016 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780016 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 249) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 250) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 251) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 252) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780016 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 Building ZINC001290780016 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780016 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 249) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 250) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 28, 50, 28, 19, 8, 19, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 251) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 252) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001290780016.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780016 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 29, 50, 29, 22, 8, 22, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780016 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780016 Building ZINC001290780018 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780018 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/253 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/254 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/255 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/255' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/256 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/256' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780018 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 Building ZINC001290780018 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780018 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 253) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 254) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 255) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 256) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780018 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 Building ZINC001290780018 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780018 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 253) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 254) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 255) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 256) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780018 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 Building ZINC001290780018 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001290780018 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 253) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 254) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 30, 50, 30, 22, 8, 22, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 255) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 256) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](O)C1) `ZINC001290780018.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001290780018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001290780018 none CCN(C)CCC(=O)N1CC[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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 10, 5, 5, 5, 1, 11, 8, 5, 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, 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, 6, 7, 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, 50, 31, 50, 31, 20, 9, 20, 9, 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, 31, 31, 31, 31, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [48, 50, 51, 49, 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, 42, 52, 53, 54]) total number of confs: 206 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290780018 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290780018 Building ZINC001290811445 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290811445 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/257 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290811445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290811445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290811445 none CC(=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.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, 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, 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, 50, 48, 19, 9, 19, 9, 9, 9, 9, 9, 3, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 48, 48, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/258 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290811445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290811445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290811445 none CC(=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.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, 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, 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, 50, 48, 18, 8, 18, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 48, 48, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290811445 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 Building ZINC001290811445 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290811445 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 257) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290811445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290811445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290811445 none CC(=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.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, 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, 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, 50, 48, 19, 9, 19, 9, 9, 9, 9, 9, 3, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 48, 48, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 258) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290811445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290811445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290811445 none CC(=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.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, 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, 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, 50, 48, 18, 8, 18, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 48, 48, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290811445 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290811445 Building ZINC001290812360 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290812360 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/259 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290812360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290812360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290812360 none CNC(=O)CC(=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', '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, 8, 1, 11, 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, 4, 7, 6, 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, 36, 50, 12, 6, 12, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 36, 36, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/260 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290812360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290812360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290812360 none CNC(=O)CC(=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', '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, 8, 1, 11, 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, 4, 7, 6, 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, 38, 50, 11, 6, 11, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 38, 38, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290812360 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 Building ZINC001290812360 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290812360 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 259) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290812360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290812360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290812360 none CNC(=O)CC(=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', '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, 8, 1, 11, 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, 4, 7, 6, 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, 36, 50, 12, 6, 12, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 36, 36, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 260) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@]2(C)C1) `ZINC001290812360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290812360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001290812360 none CNC(=O)CC(=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', '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, 8, 1, 11, 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, 4, 7, 6, 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, 38, 50, 11, 6, 11, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 38, 38, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290812360 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290812360 Building ZINC001306906578 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306906578 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/261 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001306906578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306906578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001306906578 none O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/262 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001306906578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306906578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001306906578 none O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 23, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 3, 3] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001306906578 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 Building ZINC001306906578 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306906578 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 261) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001306906578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306906578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001306906578 none O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 262) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001306906578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306906578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001306906578 none O=C(N1CCOC2(CCS(=O)(=O)CC2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 23, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 1, 3, 3] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001306906578 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001306906578 Building ZINC001290975110 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290975110 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/263 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/263' -> `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]1CNC(=O)[C@@]1(F)CCOC1) `ZINC001290975110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290975110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975110 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 36, 36, 37, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/264 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/264' -> `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]1CNC(=O)[C@@]1(F)CCOC1) `ZINC001290975110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290975110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975110 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 35, 35, 36, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 35, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290975110 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 Building ZINC001290975110 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290975110 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 263) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(F)CCOC1) `ZINC001290975110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290975110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975110 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 36, 36, 37, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 264) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(F)CCOC1) `ZINC001290975110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290975110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975110 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 20, 35, 35, 36, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 35, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290975110 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975110 Building ZINC001290975117 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290975117 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/265 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/265' -> `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]1CNC(=O)[C@]1(F)CCOC1) `ZINC001290975117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290975117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975117 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 23, 42, 42, 42, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/266 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/266' -> `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]1CNC(=O)[C@]1(F)CCOC1) `ZINC001290975117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290975117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975117 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 23, 38, 38, 39, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290975117 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 Building ZINC001290975117 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001290975117 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 265) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(F)CCOC1) `ZINC001290975117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001290975117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975117 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 23, 42, 42, 42, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 266) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(F)CCOC1) `ZINC001290975117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001290975117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001290975117 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)[C@]1(F)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 23, 38, 38, 39, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001290975117 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001290975117 Building ZINC001291583599 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291583599 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/267 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001291583599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291583599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291583599 none C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 26, 26, 50, 50, 50, 50, 50, 22, 15, 22, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/268 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001291583599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291583599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291583599 none C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 24, 24, 50, 50, 50, 50, 50, 20, 15, 20, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291583599 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 Building ZINC001291583599 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291583599 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 267) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001291583599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291583599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291583599 none C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 26, 26, 50, 50, 50, 50, 50, 22, 15, 22, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 268) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001291583599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291583599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291583599 none C[C@@H]1CN(C(=O)Cn2nccn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 24, 24, 50, 50, 50, 50, 50, 20, 15, 20, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 20, 20, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291583599 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291583599 Building ZINC001291638781 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291638781 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/269 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/269' -> `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)c1cnn[nH]1) `ZINC001291638781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291638781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001291638781 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1cnn[nH]1 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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 25, 46, 46, 46, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 25, 25, 46, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/270 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/270' -> `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)c1cnn[nH]1) `ZINC001291638781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291638781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001291638781 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1cnn[nH]1 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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 26, 48, 48, 48, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 26, 26, 48, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291638781 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 Building ZINC001291638781 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291638781 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 269) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1cnn[nH]1) `ZINC001291638781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291638781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001291638781 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1cnn[nH]1 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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 25, 46, 46, 46, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 25, 25, 46, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 270) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1cnn[nH]1) `ZINC001291638781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291638781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001291638781 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CCNC(=O)c1cnn[nH]1 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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 26, 48, 48, 48, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 26, 26, 48, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291638781 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291638781 Building ZINC001291690658 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291690658 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/271 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001291690658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291690658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291690658 none CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 10, 10, 10, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 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]) total number of confs: 162 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/272 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001291690658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291690658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291690658 none CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 12, 12, 12, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291690658 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 Building ZINC001291690658 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291690658 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 271) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001291690658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291690658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291690658 none CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 10, 10, 10, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 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]) total number of confs: 162 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 272) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001291690658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291690658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291690658 none CC(C)(C)C(=O)NCc1cn(C2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 12, 12, 12, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291690658 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291690658 Building ZINC001291691194 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291691194 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/273 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn2)C1) `ZINC001291691194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291691194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291691194 none CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 35, 38, 35, 35, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/274 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn2)C1) `ZINC001291691194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291691194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291691194 none CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 36, 33, 36, 33, 33, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291691194 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 Building ZINC001291691194 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291691194 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 273) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn2)C1) `ZINC001291691194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291691194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291691194 none CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 35, 38, 35, 35, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 274) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn2)C1) `ZINC001291691194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291691194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001291691194 none CC(C)=CC(=O)N1CC(n2cc(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 36, 33, 36, 33, 33, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291691194 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291691194 Building ZINC001291747858 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291747858 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/275 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/275' -> `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@@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291747858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747858 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 21, 32, 32, 32, 32, 44, 44, 50, 50, 50, 50, 50, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 32, 32, 32, 32, 32, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/276 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/276' -> `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@@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291747858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747858 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 30, 30, 30, 30, 47, 47, 50, 50, 50, 50, 50, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291747858 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 Building ZINC001291747858 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291747858 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 275) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291747858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747858 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 21, 32, 32, 32, 32, 44, 44, 50, 50, 50, 50, 50, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 32, 32, 32, 32, 32, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 276) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291747858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747858 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 30, 30, 30, 30, 47, 47, 50, 50, 50, 50, 50, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 30, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291747858 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747858 Building ZINC001291747859 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291747859 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/277 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291747859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747859 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 36, 36, 36, 36, 45, 45, 50, 50, 50, 50, 50, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/278 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291747859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747859 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 23, 35, 35, 35, 35, 44, 44, 50, 50, 50, 50, 50, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 35, 35, 35, 35, 35, 50, 50, 50, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291747859 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 Building ZINC001291747859 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291747859 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 277) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291747859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747859 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 36, 36, 36, 36, 45, 45, 50, 50, 50, 50, 50, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 278) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1) `ZINC001291747859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291747859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291747859 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CN(C(=O)c2cnccn2)CCO1 NO_LONG_NAME dock 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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 1, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 23, 35, 35, 35, 35, 44, 44, 50, 50, 50, 50, 50, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 35, 35, 35, 35, 35, 50, 50, 50, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291747859 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291747859 Building ZINC001291748083 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291748083 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/279 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291748083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748083 none Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 26, 42, 26, 26, 26, 26, 18, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/280 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291748083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748083 none Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 26, 39, 26, 26, 26, 26, 19, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291748083 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 Building ZINC001291748083 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291748083 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 279) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291748083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748083 none Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 26, 42, 26, 26, 26, 26, 18, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 280) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291748083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748083 none Cn1cccc1C(=O)N1CCO[C@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 26, 39, 26, 26, 26, 26, 19, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291748083 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748083 Building ZINC001291748084 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291748084 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/281 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291748084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748084 none Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 32, 40, 32, 32, 32, 32, 19, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/282 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291748084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748084 none Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 32, 42, 32, 32, 32, 32, 20, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291748084 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 Building ZINC001291748084 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291748084 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 281) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291748084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748084 none Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 32, 40, 32, 32, 32, 32, 19, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 282) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001291748084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291748084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001291748084 none Cn1cccc1C(=O)N1CCO[C@@](C)(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 32, 42, 32, 32, 32, 32, 20, 32, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291748084 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291748084 Building ZINC001291764809 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291764809 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/283 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291764809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764809 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 5, 5, 5, 5, 5, 5, 16, 16, 16, 22, 22, 50, 50, 50, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/284 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291764809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764809 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 4, 4, 4, 4, 15, 15, 15, 23, 23, 48, 50, 50, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 48, 48, 50, 50, 50, 50, 50, 15, 15, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291764809 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 Building ZINC001291764809 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291764809 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 283) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291764809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764809 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 5, 5, 5, 5, 5, 5, 16, 16, 16, 22, 22, 50, 50, 50, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 284) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291764809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764809 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 4, 4, 4, 4, 15, 15, 15, 23, 23, 48, 50, 50, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 48, 48, 50, 50, 50, 50, 50, 15, 15, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291764809 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764809 Building ZINC001291764810 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291764810 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/285 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291764810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764810 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 5, 5, 5, 5, 5, 5, 14, 14, 14, 22, 22, 49, 50, 50, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 14, 14, 14, 49, 49, 50, 50, 50, 50, 50, 14, 14, 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/286 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291764810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764810 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 5, 5, 5, 5, 5, 5, 16, 16, 16, 22, 22, 49, 50, 50, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 16, 49, 49, 50, 50, 50, 50, 50, 16, 16, 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291764810 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 Building ZINC001291764810 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291764810 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 285) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291764810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764810 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 5, 5, 5, 5, 5, 5, 14, 14, 14, 22, 22, 49, 50, 50, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 14, 14, 14, 49, 49, 50, 50, 50, 50, 50, 14, 14, 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 286) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1) `ZINC001291764810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291764810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291764810 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC(=O)N(C2CN(C(=O)CC3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 5, 5, 5, 5, 5, 5, 16, 16, 16, 22, 22, 49, 50, 50, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 16, 49, 49, 50, 50, 50, 50, 50, 16, 16, 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]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291764810 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291764810 Building ZINC001291824897 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291824897 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/287 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1) `ZINC001291824897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291824897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824897 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 41, 41, 50, 50, 50, 50, 50] 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]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/288 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1) `ZINC001291824897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291824897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824897 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 45, 45, 50, 50, 50, 50, 50] 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]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291824897 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 Building ZINC001291824897 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291824897 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 287) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1) `ZINC001291824897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291824897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824897 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 41, 41, 50, 50, 50, 50, 50] 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]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 288) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1) `ZINC001291824897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291824897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824897 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 22, 22, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 45, 45, 50, 50, 50, 50, 50] 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]) total number of confs: 180 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291824897 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824897 Building ZINC001291824898 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291824898 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/289 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1) `ZINC001291824898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291824898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824898 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 41, 41, 50, 50, 50, 50, 50] 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]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/290 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1) `ZINC001291824898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291824898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824898 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 42, 42, 50, 50, 50, 50, 50] 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]) total number of confs: 172 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291824898 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 Building ZINC001291824898 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291824898 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 289) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1) `ZINC001291824898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291824898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824898 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 41, 41, 50, 50, 50, 50, 50] 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]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 290) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1) `ZINC001291824898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291824898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291824898 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 42, 42, 50, 50, 50, 50, 50] 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]) total number of confs: 172 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291824898 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291824898 Building ZINC001291825042 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825042 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/291 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=O) `ZINC001291825042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 41, 41, 50, 50, 50, 50, 50] 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/292 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=O) `ZINC001291825042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 42, 42, 50, 50, 50, 50, 50] 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]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825042 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 Building ZINC001291825042 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825042 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 291) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=O) `ZINC001291825042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 41, 41, 50, 50, 50, 50, 50] 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]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 292) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=O) `ZINC001291825042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 42, 42, 50, 50, 50, 50, 50] 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]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825042 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825042 Building ZINC001291825044 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825044 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/293 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/293' -> `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[C@@H]1CCNC1=O) `ZINC001291825044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825044 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 42, 42, 50, 50, 50, 50, 50] 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]) total number of confs: 174 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/294 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/294' -> `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[C@@H]1CCNC1=O) `ZINC001291825044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825044 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 20, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 44, 44, 50, 50, 50, 50, 50] 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]) total number of confs: 179 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825044 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 Building ZINC001291825044 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825044 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 293) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCNC1=O) `ZINC001291825044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825044 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 42, 42, 50, 50, 50, 50, 50] 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]) total number of confs: 174 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 294) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCNC1=O) `ZINC001291825044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825044 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1CCNC1=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', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 20, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 44, 44, 50, 50, 50, 50, 50] 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]) total number of confs: 179 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825044 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825044 Building ZINC001291825058 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825058 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/295 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)nnn1C) `ZINC001291825058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001291825058 none Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 39, 15, 15, 15, 15, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50] 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: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/296 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)nnn1C) `ZINC001291825058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001291825058 none Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 37, 17, 17, 17, 17, 17, 17, 17, 2, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825058 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 Building ZINC001291825058 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825058 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 295) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)nnn1C) `ZINC001291825058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001291825058 none Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C3)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 39, 15, 15, 15, 15, 15, 15, 15, 2, 15, 2, 1, 2, 1, 1, 1, 2, 2, 2, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50] 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: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 296) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)nnn1C) `ZINC001291825058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001291825058 none Cc1c(C(=O)N2[C@@H]3CC[C@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C3)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 37, 17, 17, 17, 17, 17, 17, 17, 2, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825058 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825058 Building ZINC001291825071 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825071 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/297 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/297' -> `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)c1nccnc1N) `ZINC001291825071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825071 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1nccnc1N NO_LONG_NAME dock atom 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/298 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/298' -> `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)c1nccnc1N) `ZINC001291825071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825071 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1nccnc1N NO_LONG_NAME dock atom 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 42, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825071 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 Building ZINC001291825071 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825071 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 297) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1nccnc1N) `ZINC001291825071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825071 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1nccnc1N NO_LONG_NAME dock atom 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 40, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 298) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1nccnc1N) `ZINC001291825071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825071 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1nccnc1N NO_LONG_NAME dock atom 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 42, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 19, 19, 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]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825071 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825071 Building ZINC001291825390 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825390 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/299 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/299' -> `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)Cc1cncnc1) `ZINC001291825390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825390 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)Cc1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 183 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/300 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/300' -> `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)Cc1cncnc1) `ZINC001291825390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825390 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)Cc1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 20, 49, 50, 50, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 49, 49, 50, 49, 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]) total number of confs: 190 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825390 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 Building ZINC001291825390 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825390 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 299) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)Cc1cncnc1) `ZINC001291825390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825390 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)Cc1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 183 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 300) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)Cc1cncnc1) `ZINC001291825390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825390 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)Cc1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 20, 49, 50, 50, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 49, 49, 50, 49, 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]) total number of confs: 190 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825390 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825390 Building ZINC001291825397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/301 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/301' -> `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)c1cncnc1) `ZINC001291825397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001291825397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 26, 26, 26, 26, 26, 26, 50, 45, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/302 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/302' -> `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)c1cncnc1) `ZINC001291825397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001291825397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 49, 49, 50, 50, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 30, 30, 30, 30, 30, 30, 50, 49, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 Building ZINC001291825397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 301) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cncnc1) `ZINC001291825397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001291825397 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 45, 45, 50, 50, 45, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 26, 26, 26, 26, 26, 26, 50, 45, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 302) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cncnc1) `ZINC001291825397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001291825397 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)c1cncnc1 NO_LONG_NAME dock atom 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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 49, 49, 50, 50, 49, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 30, 30, 30, 30, 30, 30, 50, 49, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825397 Building ZINC001291825789 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825789 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/303 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/303' -> `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]1CCC(=O)N1) `ZINC001291825789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825789 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 38, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/304 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/304' -> `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]1CCC(=O)N1) `ZINC001291825789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825789 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 33, 38, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825789 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 Building ZINC001291825789 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291825789 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 303) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCC(=O)N1) `ZINC001291825789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291825789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825789 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 38, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 304) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCC(=O)N1) `ZINC001291825789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291825789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291825789 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom 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', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 33, 38, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291825789 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291825789 Building ZINC001291901457 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291901457 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/305 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2) `ZINC001291901457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291901457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291901457 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 37, 37, 37, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 37, 37, 37, 37, 37, 37, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/306 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2) `ZINC001291901457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291901457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291901457 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 38, 38, 38, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 38, 38, 38, 38, 38, 38, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291901457 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 Building ZINC001291901457 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291901457 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 305) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2) `ZINC001291901457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291901457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291901457 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 37, 37, 37, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 37, 37, 37, 37, 37, 37, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 306) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2) `ZINC001291901457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291901457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291901457 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C(C)(C)C(N)=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 38, 38, 38, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 38, 38, 38, 38, 38, 38, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291901457 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291901457 Building ZINC001316649903 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001316649903 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/307 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001316649903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649903 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 41, 41, 41, 41, 14, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/308 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001316649903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649903 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 42, 42, 17, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 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/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001316649903 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 Building ZINC001316649903 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001316649903 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 307) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001316649903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649903 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 41, 41, 41, 41, 14, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 149 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 308) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001316649903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649903 none C[C@@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 42, 42, 17, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 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/13323/xbn-8058097.40/working/building/ZINC001316649903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001316649903 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649903 Building ZINC001316649904 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001316649904 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/309 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001316649904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649904 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 49, 49, 49, 49, 40, 40, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/310 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001316649904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649904 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 48, 44, 44, 44, 44, 44, 13, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 48, 50, 50, 50, 50, 48, 48, 48, 47, 44, 44, 44, 44, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001316649904 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 Building ZINC001316649904 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001316649904 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 309) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001316649904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649904 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 49, 50, 50, 50, 50, 49, 49, 49, 49, 40, 40, 40, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 310) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C) `ZINC001316649904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001316649904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001316649904 none C[C@H](N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 48, 44, 44, 44, 44, 44, 13, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 48, 50, 50, 50, 50, 48, 48, 48, 47, 44, 44, 44, 44, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001316649904 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001316649904 Building ZINC001291964194 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291964194 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/311 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001291964194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291964194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964194 none C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 21, 44, 44, 49, 50, 50, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 44, 44, 49, 49, 50, 50, 21, 7, 7, 7, 7, 7, 7, 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: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/312 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/312' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001291964194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291964194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964194 none C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 44, 44, 48, 50, 50, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 44, 44, 44, 48, 48, 50, 50, 22, 6, 6, 6, 6, 6, 6, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291964194 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 Building ZINC001291964194 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291964194 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 311) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001291964194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291964194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964194 none C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 21, 44, 44, 49, 50, 50, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 44, 44, 49, 49, 50, 50, 21, 7, 7, 7, 7, 7, 7, 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: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 312) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001291964194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291964194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964194 none C[C@@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 44, 44, 48, 50, 50, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 44, 44, 44, 48, 48, 50, 50, 22, 6, 6, 6, 6, 6, 6, 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291964194 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964194 Building ZINC001291964195 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291964195 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/313 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001291964195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291964195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964195 none C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 45, 45, 49, 50, 50, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 45, 45, 49, 49, 50, 50, 26, 7, 7, 7, 7, 7, 7, 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: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/314 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001291964195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291964195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964195 none C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 43, 43, 50, 50, 50, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 43, 43, 43, 50, 50, 50, 50, 24, 6, 6, 6, 6, 6, 6, 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: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291964195 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 Building ZINC001291964195 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291964195 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 313) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001291964195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291964195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964195 none C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 45, 45, 49, 50, 50, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 45, 45, 49, 49, 50, 50, 26, 7, 7, 7, 7, 7, 7, 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: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 314) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001291964195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291964195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001291964195 none C[C@H](CC(N)=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 43, 43, 50, 50, 50, 24, 24, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 43, 43, 43, 50, 50, 50, 50, 24, 6, 6, 6, 6, 6, 6, 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: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291964195 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291964195 Building ZINC001291988723 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291988723 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/315 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2) `ZINC001291988723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291988723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291988723 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 42, 50, 50, 42, 42, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 50, 50, 42, 42, 42, 42, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/316 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2) `ZINC001291988723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291988723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291988723 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 40, 50, 50, 40, 40, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 50, 50, 40, 40, 40, 40, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291988723 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 Building ZINC001291988723 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001291988723 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 315) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2) `ZINC001291988723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001291988723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291988723 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 42, 50, 50, 42, 42, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 50, 50, 42, 42, 42, 42, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 316) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2) `ZINC001291988723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001291988723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001291988723 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1(C(N)=O)CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 40, 50, 50, 40, 40, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 50, 50, 40, 40, 40, 40, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001291988723 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001291988723 Building ZINC001292008454 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292008454 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/317 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2) `ZINC001292008454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292008454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292008454 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 35, 46, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 35, 35, 46, 46, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/318 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2) `ZINC001292008454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292008454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292008454 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 41, 45, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 41, 41, 45, 45, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292008454 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 Building ZINC001292008454 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292008454 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 317) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2) `ZINC001292008454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292008454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292008454 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 35, 46, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 35, 35, 46, 46, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 318) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2) `ZINC001292008454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292008454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292008454 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)CCc1cnn[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 41, 45, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 41, 41, 45, 45, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292008454 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292008454 Building ZINC001292061935 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292061935 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/319 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/319' -> `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)C1=COCCO1) `ZINC001292061935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292061935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292061935 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=COCCO1 NO_LONG_NAME dock atom 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.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/320 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/320' -> `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)C1=COCCO1) `ZINC001292061935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292061935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292061935 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=COCCO1 NO_LONG_NAME dock atom 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.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 27, 27, 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 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292061935 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 Building ZINC001292061935 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292061935 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 319) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=COCCO1) `ZINC001292061935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292061935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292061935 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=COCCO1 NO_LONG_NAME dock atom 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.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 320) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=COCCO1) `ZINC001292061935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292061935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292061935 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=COCCO1 NO_LONG_NAME dock atom 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.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 27, 27, 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 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292061935 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292061935 Building ZINC001292063145 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063145 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/321 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/322 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/323 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/323' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/324 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/324' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063145 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 Building ZINC001292063145 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063145 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 321) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 322) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 323) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 324) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063145 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 Building ZINC001292063145 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063145 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 321) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 322) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 323) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 324) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063145 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 Building ZINC001292063145 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063145 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 321) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 322) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 323) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 12, 36, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 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, 51, 52]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 324) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063145.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063145 none CN1CCC[C@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 50, 11, 31, 11, 11, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063145 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063145 Building ZINC001292063146 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063146 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/325 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/326 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/327 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/327' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/328 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/328' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063146 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 Building ZINC001292063146 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063146 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 325) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 326) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 327) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 328) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063146 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 Building ZINC001292063146 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063146 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 325) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 326) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 327) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 328) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063146 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 Building ZINC001292063146 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001292063146 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 325) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 326) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 327) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 10, 33, 10, 10, 10, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 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, 51, 52]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 328) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001292063146.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001292063146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001292063146 none CN1CCC[C@@H]1C(=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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 8, 33, 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, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 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: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063146 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063146 Building ZINC001292063356 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292063356 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/329 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=O) `ZINC001292063356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063356 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 33, 41, 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 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]) total number of confs: 133 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/330 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=O) `ZINC001292063356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063356 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 34, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 121 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063356 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 Building ZINC001292063356 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292063356 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 329) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=O) `ZINC001292063356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063356 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 33, 41, 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 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]) total number of confs: 133 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 330) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=O) `ZINC001292063356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063356 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 34, 44, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 121 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063356 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063356 Building ZINC001292063357 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292063357 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/331 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=O) `ZINC001292063357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063357 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 136 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/332 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=O) `ZINC001292063357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063357 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 38, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063357 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 Building ZINC001292063357 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292063357 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 331) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=O) `ZINC001292063357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063357 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50] 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]) total number of confs: 136 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 332) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=O) `ZINC001292063357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063357 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CCCNC1=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 38, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063357 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063357 Building ZINC001292063370 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292063370 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/333 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/333' -> `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)CCn1ccnn1) `ZINC001292063370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063370 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CCn1ccnn1 NO_LONG_NAME dock atom 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 37, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 37, 37, 43, 43, 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]) total number of confs: 186 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/334 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/334' -> `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)CCn1ccnn1) `ZINC001292063370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063370 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CCn1ccnn1 NO_LONG_NAME dock atom 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 37, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 37, 37, 47, 47, 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]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063370 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 Building ZINC001292063370 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292063370 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 333) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CCn1ccnn1) `ZINC001292063370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292063370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063370 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CCn1ccnn1 NO_LONG_NAME dock atom 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 37, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 37, 37, 43, 43, 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]) total number of confs: 186 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 334) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CCn1ccnn1) `ZINC001292063370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292063370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292063370 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CCn1ccnn1 NO_LONG_NAME dock atom 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 37, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 37, 37, 47, 47, 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]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292063370 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292063370 Building ZINC001292064068 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292064068 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/335 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/335' -> `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)CN1CCCC1) `ZINC001292064068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292064068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292064068 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1CCCC1 NO_LONG_NAME dock atom 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', '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'] 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, 10, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 26, 26, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/336 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/336' -> `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)CN1CCCC1) `ZINC001292064068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292064068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292064068 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1CCCC1 NO_LONG_NAME dock atom 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', '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'] 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, 10, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292064068 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 Building ZINC001292064068 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292064068 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 335) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1CCCC1) `ZINC001292064068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292064068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292064068 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1CCCC1 NO_LONG_NAME dock atom 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', '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'] 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, 10, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 26, 26, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 336) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1CCCC1) `ZINC001292064068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292064068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292064068 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1CCCC1 NO_LONG_NAME dock atom 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', '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'] 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, 10, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 43, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292064068 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292064068 Building ZINC001292266170 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292266170 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/337 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2) `ZINC001292266170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292266170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292266170 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2 NO_LONG_NAME dock 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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 41, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 41, 41, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/338 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2) `ZINC001292266170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292266170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292266170 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2 NO_LONG_NAME dock 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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 39, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 39, 39, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292266170 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 Building ZINC001292266170 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292266170 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 337) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2) `ZINC001292266170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292266170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292266170 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2 NO_LONG_NAME dock 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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 41, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 41, 41, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 338) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2) `ZINC001292266170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292266170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292266170 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]12CCC[C@H]1CN(C(=O)Cn1cncn1)C2 NO_LONG_NAME dock 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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 8, 8, 16, 16, 39, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 39, 39, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292266170 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292266170 Building ZINC001292303353 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292303353 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/339 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292303353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303353 none NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 20, 12, 12, 12, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 20, 20, 12, 12, 4, 4, 12, 12, 12, 12] 27 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]) total number of confs: 53 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/340 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292303353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303353 none NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 38, 17, 17, 17, 7, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 38, 38, 17, 17, 8, 8, 17, 17, 17, 17] 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292303353 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 Building ZINC001292303353 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292303353 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 339) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292303353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303353 none NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 20, 12, 12, 12, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 20, 20, 12, 12, 4, 4, 12, 12, 12, 12] 27 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]) total number of confs: 53 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 340) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292303353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303353 none NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 38, 17, 17, 17, 7, 2, 8, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 38, 38, 17, 17, 8, 8, 17, 17, 17, 17] 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292303353 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303353 Building ZINC001292303365 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292303365 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/341 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292303365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303365 none NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 35, 15, 15, 15, 7, 1, 9, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 35, 35, 15, 15, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/342 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292303365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303365 none NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 15, 36, 15, 15, 15, 7, 1, 10, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 36, 36, 15, 15, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292303365 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 Building ZINC001292303365 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292303365 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 341) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292303365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303365 none NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 35, 15, 15, 15, 7, 1, 9, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 15, 35, 35, 15, 15, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 342) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1) `ZINC001292303365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292303365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001292303365 none NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 15, 36, 15, 15, 15, 7, 1, 10, 1, 1, 1, 9, 9, 9, 9, 9, 15, 15, 15, 36, 36, 15, 15, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292303365 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292303365 Building ZINC001292391781 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292391781 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/343 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1) `ZINC001292391781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292391781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292391781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 11, 12, 12, 12, 12, 17, 17, 26, 31, 31, 31, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 31, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/344 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1) `ZINC001292391781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292391781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292391781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 12, 14, 14, 13, 14, 16, 16, 26, 32, 32, 32, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 32, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292391781 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 Building ZINC001292391781 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292391781 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 343) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1) `ZINC001292391781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292391781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292391781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 11, 12, 12, 12, 12, 17, 17, 26, 31, 31, 31, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 31, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 344) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1) `ZINC001292391781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292391781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292391781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)c2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 12, 14, 14, 13, 14, 16, 16, 26, 32, 32, 32, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 32, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292391781 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391781 Building ZINC001292391811 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292391811 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/345 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CC1) `ZINC001292391811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292391811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001292391811 none CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 50, 36, 18, 36, 18, 18, 18, 9, 2, 14, 1, 1, 1, 1, 1, 1, 18, 18, 41, 41, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/346 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CC1) `ZINC001292391811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292391811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001292391811 none CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 19, 38, 19, 19, 19, 10, 2, 14, 1, 1, 1, 1, 1, 1, 19, 19, 43, 43, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 43, 43, 43, 43] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292391811 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 Building ZINC001292391811 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292391811 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 345) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CC1) `ZINC001292391811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292391811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001292391811 none CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 50, 36, 18, 36, 18, 18, 18, 9, 2, 14, 1, 1, 1, 1, 1, 1, 18, 18, 41, 41, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 41, 41, 41, 41] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 346) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CC1) `ZINC001292391811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292391811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001292391811 none CN(C)C(=O)C1(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 19, 38, 19, 19, 19, 10, 2, 14, 1, 1, 1, 1, 1, 1, 19, 19, 43, 43, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 43, 43, 43, 43] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292391811 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292391811 Building ZINC001292392750 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292392750 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/347 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292392750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392750 none CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 27, 39, 39, 50, 50, 13, 27, 13, 13, 13, 9, 2, 12, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 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]) total number of confs: 194 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/348 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292392750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392750 none CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 37, 30, 37, 37, 50, 50, 14, 30, 14, 14, 14, 8, 2, 12, 1, 1, 1, 1, 1, 1, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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]) total number of confs: 198 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292392750 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 Building ZINC001292392750 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292392750 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 347) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292392750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392750 none CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 27, 39, 39, 50, 50, 13, 27, 13, 13, 13, 9, 2, 12, 1, 1, 1, 1, 1, 1, 13, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 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]) total number of confs: 194 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 348) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292392750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392750 none CC(C)C[C@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 37, 30, 37, 37, 50, 50, 14, 30, 14, 14, 14, 8, 2, 12, 1, 1, 1, 1, 1, 1, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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]) total number of confs: 198 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292392750 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392750 Building ZINC001292392751 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292392751 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/349 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292392751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392751 none CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 37, 25, 37, 37, 49, 49, 13, 25, 13, 13, 13, 8, 2, 11, 1, 1, 1, 1, 1, 1, 13, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 49, 49, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 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]) total number of confs: 197 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/350 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292392751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392751 none CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 38, 27, 38, 38, 48, 48, 14, 27, 14, 14, 14, 8, 2, 12, 1, 1, 1, 1, 1, 1, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 48, 48, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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]) total number of confs: 194 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292392751 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 Building ZINC001292392751 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292392751 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 349) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292392751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392751 none CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 37, 25, 37, 37, 49, 49, 13, 25, 13, 13, 13, 8, 2, 11, 1, 1, 1, 1, 1, 1, 13, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 49, 49, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 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]) total number of confs: 197 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 350) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292392751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292392751 none CC(C)C[C@@H](C(N)=O)C(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 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, 7, 7, 7, 7, 7, 7, 4, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 38, 27, 38, 38, 48, 48, 14, 27, 14, 14, 14, 8, 2, 12, 1, 1, 1, 1, 1, 1, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 48, 48, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 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]) total number of confs: 194 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292392751 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392751 Building ZINC001292392762 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292392762 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/351 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292392762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001292392762 none COCCOCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 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, 30, 17, 17, 11, 8, 11, 8, 8, 8, 7, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 49, 49, 17, 17, 17, 17, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/352 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292392762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001292392762 none COCCOCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 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, 24, 16, 16, 12, 6, 12, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 47, 47, 16, 16, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292392762 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 Building ZINC001292392762 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292392762 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 351) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292392762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001292392762 none COCCOCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 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, 30, 17, 17, 11, 8, 11, 8, 8, 8, 7, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 49, 49, 17, 17, 17, 17, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 352) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292392762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292392762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001292392762 none COCCOCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 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, 24, 16, 16, 12, 6, 12, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 47, 47, 16, 16, 16, 16, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292392762 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292392762 Building ZINC001292393010 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292393010 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/353 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292393010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292393010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292393010 none CNC(=O)CCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 19, 8, 7, 8, 7, 7, 7, 5, 2, 6, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 42, 41, 22, 22, 19, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/354 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292393010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292393010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292393010 none CNC(=O)CCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 23, 19, 10, 6, 10, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 40, 40, 23, 23, 19, 19, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292393010 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 Building ZINC001292393010 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292393010 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 353) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292393010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292393010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292393010 none CNC(=O)CCCC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 19, 8, 7, 8, 7, 7, 7, 5, 2, 6, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 42, 41, 22, 22, 19, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 354) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001292393010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292393010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292393010 none CNC(=O)CCCC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 23, 19, 10, 6, 10, 6, 6, 6, 4, 2, 5, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 40, 40, 23, 23, 19, 19, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292393010 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393010 Building ZINC001292393013 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292393013 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/355 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1) `ZINC001292393013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292393013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292393013 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 14, 14, 19, 21, 21, 21, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 21, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/356 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1) `ZINC001292393013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292393013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292393013 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 12, 12, 18, 22, 22, 23, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292393013 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 Building ZINC001292393013 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292393013 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 355) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1) `ZINC001292393013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292393013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292393013 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 14, 14, 19, 21, 21, 21, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 21, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 356) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1) `ZINC001292393013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292393013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292393013 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)CNC(=O)C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 12, 12, 18, 22, 22, 23, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 22, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292393013 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292393013 Building ZINC001292446702 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292446702 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/357 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/357' -> `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)Nc1cnn(C(F)F)c1) `ZINC001292446702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292446702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001292446702 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C(F)F)c1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', '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, 1, 1, 8, 8, 5, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 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: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 19, 19, 10, 4, 4, 4, 4, 13, 13, 4, 2, 10, 19, 10] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/358 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/358' -> `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)Nc1cnn(C(F)F)c1) `ZINC001292446702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292446702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001292446702 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(C(F)F)c1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', '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, 1, 1, 8, 8, 5, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 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: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 19, 19, 10, 4, 4, 4, 4, 13, 13, 4, 2, 10, 19, 10] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292446702 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 Building ZINC001292446702 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292446702 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 357) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C(F)F)c1) `ZINC001292446702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292446702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001292446702 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C(F)F)c1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', '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, 1, 1, 8, 8, 5, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 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: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 19, 19, 10, 4, 4, 4, 4, 13, 13, 4, 2, 10, 19, 10] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 358) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(C(F)F)c1) `ZINC001292446702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292446702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001292446702 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cnn(C(F)F)c1 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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', '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, 1, 1, 8, 8, 5, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 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: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 19, 19, 10, 4, 4, 4, 4, 13, 13, 4, 2, 10, 19, 10] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292446702 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292446702 Building ZINC001292588192 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588192 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/359 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1) `ZINC001292588192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588192 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 8, 17, 17, 17, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 17, 35, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/360 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1) `ZINC001292588192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588192 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 8, 17, 17, 17, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 17, 36, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588192 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 Building ZINC001292588192 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588192 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 359) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1) `ZINC001292588192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588192 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 8, 17, 17, 17, 35, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 17, 35, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 360) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1) `ZINC001292588192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588192 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1c[nH]nc1c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 6, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 8, 17, 17, 17, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 17, 36, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588192 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588192 Building ZINC001292588242 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588242 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/361 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1) `ZINC001292588242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292588242 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 31, 31, 31, 34, 34, 34, 34, 50, 50, 50, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 19, 31, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/362 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1) `ZINC001292588242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292588242 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 31, 31, 31, 34, 34, 34, 34, 50, 50, 50, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 19, 31, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588242 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 Building ZINC001292588242 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588242 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 361) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1) `ZINC001292588242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292588242 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 31, 31, 31, 34, 34, 34, 34, 50, 50, 50, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 19, 31, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 362) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1) `ZINC001292588242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292588242 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccn(CC(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 5, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 31, 31, 31, 34, 34, 34, 34, 50, 50, 50, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 19, 19, 31, 34, 34, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588242 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588242 Building ZINC001292588249 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588249 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/363 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292588249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588249 none CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 49, 50, 28, 28, 28, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 28, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 211 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/364 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292588249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588249 none CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 45, 50, 23, 23, 23, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 23, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588249 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 Building ZINC001292588249 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588249 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 363) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292588249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588249 none CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 49, 50, 28, 28, 28, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 28, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 211 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 364) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292588249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588249 none CC(=O)N1CCCC[C@@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 45, 50, 23, 23, 23, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 23, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 215 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588249 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588249 Building ZINC001292588250 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588250 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/365 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292588250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588250 none CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 46, 50, 26, 26, 26, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/366 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292588250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588250 none CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 49, 50, 27, 27, 27, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 27, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 208 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588250 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 Building ZINC001292588250 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588250 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 365) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292588250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588250 none CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 46, 50, 26, 26, 26, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 366) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292588250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292588250 none CC(=O)N1CCCC[C@H]1CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 1, 11, 8, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 49, 50, 27, 27, 27, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 27, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 208 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588250 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588250 Building ZINC001292588253 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588253 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/367 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1) `ZINC001292588253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588253 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 20, 20, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/368 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1) `ZINC001292588253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588253 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 20, 20, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588253 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 Building ZINC001292588253 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588253 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 367) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1) `ZINC001292588253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588253 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 20, 20, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 368) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1) `ZINC001292588253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588253 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccncc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 20, 20, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588253 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588253 Building ZINC001292588276 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588276 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/369 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1) `ZINC001292588276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588276 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/370 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1) `ZINC001292588276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588276 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588276 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 Building ZINC001292588276 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588276 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 369) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1) `ZINC001292588276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588276 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 370) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1) `ZINC001292588276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588276 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ncn(c2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588276 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588276 Building ZINC001292588285 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588285 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/371 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1) `ZINC001292588285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588285 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 6, 14, 14, 14, 40, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 6, 6, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/372 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1) `ZINC001292588285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588285 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 6, 14, 14, 14, 41, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 6, 6, 14, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588285 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 Building ZINC001292588285 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588285 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 371) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1) `ZINC001292588285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588285 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 6, 14, 14, 14, 40, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 6, 6, 14, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 372) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1) `ZINC001292588285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588285 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)Cn1cc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 6, 14, 14, 14, 41, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 6, 6, 14, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588285 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588285 Building ZINC001292588293 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588293 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/373 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1) `ZINC001292588293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588293 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 16, 22, 22, 22, 34, 34, 22, 22, 50, 50, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 16, 16, 22, 34, 34, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/374 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1) `ZINC001292588293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588293 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 22, 22, 22, 34, 34, 22, 22, 50, 50, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 22, 34, 34, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588293 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 Building ZINC001292588293 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588293 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 373) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1) `ZINC001292588293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588293 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 16, 22, 22, 22, 34, 34, 22, 22, 50, 50, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 16, 16, 22, 34, 34, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 374) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1) `ZINC001292588293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588293 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 22, 22, 22, 34, 34, 22, 22, 50, 50, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 15, 15, 22, 34, 34, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588293 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588293 Building ZINC001292588309 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588309 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/375 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1) `ZINC001292588309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 30, 30, 30, 31, 31, 37, 37, 37, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 17, 17, 30, 31, 31, 31, 31, 37, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/376 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1) `ZINC001292588309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 30, 30, 30, 31, 31, 39, 39, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 17, 17, 30, 31, 31, 31, 31, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588309 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 Building ZINC001292588309 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588309 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 375) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1) `ZINC001292588309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588309 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 30, 30, 30, 31, 31, 37, 37, 37, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 17, 17, 30, 31, 31, 31, 31, 37, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 376) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1) `ZINC001292588309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588309 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCNC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 30, 30, 30, 31, 31, 39, 39, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 17, 17, 30, 31, 31, 31, 31, 39, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588309 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588309 Building ZINC001292588324 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588324 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/377 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1) `ZINC001292588324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588324 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 36, 36, 36, 50, 50, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 24, 24, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/378 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1) `ZINC001292588324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588324 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 36, 36, 36, 50, 50, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 24, 24, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588324 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 Building ZINC001292588324 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588324 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 377) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1) `ZINC001292588324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588324 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 36, 36, 36, 50, 50, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 24, 24, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 378) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1) `ZINC001292588324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588324 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2cnnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 36, 36, 36, 50, 50, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 24, 24, 36, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588324 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588324 Building ZINC001292588347 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588347 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/379 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1) `ZINC001292588347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588347 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 27, 27, 27, 50, 50, 50, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/380 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1) `ZINC001292588347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588347 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 27, 27, 27, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 16, 27, 28, 28, 50, 50, 50, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588347 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 Building ZINC001292588347 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588347 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 379) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1) `ZINC001292588347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588347 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 27, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 27, 27, 27, 50, 50, 50, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 380) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1) `ZINC001292588347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588347 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc(n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 27, 27, 27, 28, 28, 28, 28, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 16, 16, 27, 28, 28, 50, 50, 50, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588347 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588347 Building ZINC001292588351 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588351 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/381 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)c(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001292588351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588351 none Cc1c(Cl)c(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] 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, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/382 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)c(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001292588351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588351 none Cc1c(Cl)c(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] 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, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588351 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 Building ZINC001292588351 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588351 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 381) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)c(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001292588351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588351 none Cc1c(Cl)c(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] 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, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 382) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Cl)c(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001292588351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588351 none Cc1c(Cl)c(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] 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, 40, 41, 42]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588351 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588351 Building ZINC001292588354 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588354 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/383 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2n1) `ZINC001292588354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001292588354 none Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 36, 36, 36, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/384 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2n1) `ZINC001292588354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001292588354 none Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 36, 36, 36, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588354 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 Building ZINC001292588354 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588354 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 383) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2n1) `ZINC001292588354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001292588354 none Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 36, 36, 36, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 384) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2n1) `ZINC001292588354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001292588354 none Cc1cc(C)n2nc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 36, 36, 36, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588354 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588354 Building ZINC001292588357 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588357 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/385 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588357 none C[C@@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 44, 26, 26, 26, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 44, 44, 26, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/386 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588357 none C[C@@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 44, 23, 23, 23, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 44, 44, 23, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588357 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 Building ZINC001292588357 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588357 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 385) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588357 none C[C@@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 44, 26, 26, 26, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 44, 44, 26, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 386) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588357 none C[C@@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 44, 23, 23, 23, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 44, 44, 23, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588357 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588357 Building ZINC001292588358 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588358 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/387 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588358 none C[C@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 45, 23, 23, 23, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 23, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/388 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588358 none C[C@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 44, 26, 26, 26, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 44, 44, 26, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588358 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 Building ZINC001292588358 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588358 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 387) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588358 none C[C@H](OCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 45, 23, 23, 23, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 45, 45, 23, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 388) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C) `ZINC001292588358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001292588358 none C[C@H](OCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 44, 26, 26, 26, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 44, 44, 26, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588358 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588358 Building ZINC001292588381 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588381 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/389 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1) `ZINC001292588381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588381 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 19, 19, 19, 40, 40, 40, 40, 40, 50, 50, 50, 50, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 19, 40, 40, 40, 50, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/390 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1) `ZINC001292588381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588381 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 20, 20, 20, 41, 41, 41, 41, 41, 50, 50, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 20, 41, 41, 41, 50, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588381 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 Building ZINC001292588381 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588381 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 389) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1) `ZINC001292588381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588381 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 19, 19, 19, 40, 40, 40, 40, 40, 50, 50, 50, 50, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 19, 40, 40, 40, 50, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 390) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1) `ZINC001292588381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588381 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(n2cnnn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 20, 20, 20, 41, 41, 41, 41, 41, 50, 50, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 20, 41, 41, 41, 50, 41] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588381 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588381 Building ZINC001292588421 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588421 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/391 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1) `ZINC001292588421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588421 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/392 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1) `ZINC001292588421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588421 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588421 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 Building ZINC001292588421 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588421 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 391) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1) `ZINC001292588421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588421 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 31, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 392) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1) `ZINC001292588421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588421 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccnc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588421 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588421 Building ZINC001292588455 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588455 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/393 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588455 none Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 22, 22, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/394 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588455 none Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 23, 23, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588455 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 Building ZINC001292588455 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588455 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 393) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588455 none Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 22, 22, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 394) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588455 none Cc1ncc2n1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 23, 23, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588455 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588455 Building ZINC001292588456 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588456 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/395 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588456 none Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 23, 23, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/396 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588456 none Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 23, 23, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588456 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 Building ZINC001292588456 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588456 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 395) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588456 none Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 23, 23, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 396) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292588456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588456 none Cc1ncc2n1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 23, 23, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588456 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588456 Building ZINC001292588461 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588461 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/397 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1) `ZINC001292588461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588461 none CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 36, 21, 38, 38, 14, 14, 14, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 42, 42, 38, 38, 14, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/398 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1) `ZINC001292588461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588461 none CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 25, 38, 38, 14, 14, 14, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 43, 43, 38, 38, 14, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588461 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 Building ZINC001292588461 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588461 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 397) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1) `ZINC001292588461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588461 none CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 36, 21, 38, 38, 14, 14, 14, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 42, 42, 38, 38, 14, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 398) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1) `ZINC001292588461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588461 none CC(=O)NCc1ccc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 38, 25, 38, 38, 14, 14, 14, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 43, 43, 38, 38, 14, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588461 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588461 Building ZINC001292588464 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588464 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/399 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2) `ZINC001292588464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588464 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 21, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/400 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2) `ZINC001292588464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588464 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 21, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588464 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 Building ZINC001292588464 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588464 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 399) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2) `ZINC001292588464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588464 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 21, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 400) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2) `ZINC001292588464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588464 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 21, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588464 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588464 Building ZINC001292588488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/401 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(CCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001292588488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588488 none COc1cncc(CCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 20, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/402 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(CCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001292588488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588488 none COc1cncc(CCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 21, 21, 21, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 21, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 Building ZINC001292588488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 401) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(CCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001292588488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588488 none COc1cncc(CCC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 20, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 402) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(CCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001292588488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588488 none COc1cncc(CCC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 21, 21, 21, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 21, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588488 Building ZINC001292588500 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588500 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/403 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292588500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001292588500 none Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 15, 15, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 25, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/404 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292588500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001292588500 none Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 15, 15, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 25, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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]) total number of confs: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588500 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 Building ZINC001292588500 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588500 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 403) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292588500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001292588500 none Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 15, 15, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 25, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 404) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292588500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001292588500 none Cn1ncc(C(F)(F)F)c1C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 15, 15, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 25, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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]) total number of confs: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588500 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588500 Building ZINC001292588542 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588542 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/405 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1) `ZINC001292588542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588542 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 8, 8, 8, 8, 13, 8, 18, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 13, 13, 13, 13, 14, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/406 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1) `ZINC001292588542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588542 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 7, 12, 7, 16, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 7, 7, 7, 12, 12, 12, 12, 12, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588542 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 Building ZINC001292588542 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588542 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 405) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1) `ZINC001292588542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588542 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 8, 8, 8, 8, 13, 8, 18, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 13, 13, 13, 13, 14, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 406) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1) `ZINC001292588542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292588542 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCCOC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 7, 12, 7, 16, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 7, 7, 7, 12, 12, 12, 12, 12, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588542 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588542 Building ZINC001292588560 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588560 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/407 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1) `ZINC001292588560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588560 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/408 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1) `ZINC001292588560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588560 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588560 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 Building ZINC001292588560 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588560 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 407) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1) `ZINC001292588560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588560 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 408) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1) `ZINC001292588560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588560 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cnn(c2ccccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588560 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588560 Building ZINC001292588577 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588577 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/409 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001292588577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001292588577 none Cn1nc(CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/410 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001292588577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001292588577 none Cn1nc(CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588577 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 Building ZINC001292588577 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588577 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 409) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001292588577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001292588577 none Cn1nc(CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 410) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001292588577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001292588577 none Cn1nc(CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 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]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588577 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588577 Building ZINC001292588607 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588607 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/411 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2) `ZINC001292588607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588607 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 19, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/412 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2) `ZINC001292588607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588607 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588607 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 Building ZINC001292588607 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588607 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 411) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2) `ZINC001292588607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588607 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 19, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 412) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2) `ZINC001292588607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588607 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588607 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588607 Building ZINC001292588613 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588613 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/413 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588613 none C[C@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 23, 23, 23, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 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: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/414 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588613 none C[C@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 48, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 48, 48, 48, 44, 44, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588613 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 Building ZINC001292588613 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588613 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 413) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588613 none C[C@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 23, 23, 23, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 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: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 414) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588613 none C[C@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 48, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 48, 48, 48, 44, 44, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588613 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588613 Building ZINC001292588614 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588614 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/415 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588614 none C[C@@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 47, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 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/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/416 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588614 none C[C@@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 22, 22, 22, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588614 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 Building ZINC001292588614 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588614 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 415) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588614 none C[C@@H](CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 47, 19, 19, 19, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 47, 47, 47, 43, 43, 19, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 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/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 416) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O) `ZINC001292588614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001292588614 none C[C@@H](CC(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)N1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 22, 22, 22, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588614 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588614 Building ZINC001292588623 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588623 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/417 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n2n1) `ZINC001292588623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588623 none Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.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, 1, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 50, 50, 50, 36, 36, 36, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/418 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n2n1) `ZINC001292588623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588623 none Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.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, 1, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 50, 50, 50, 36, 36, 36, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588623 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 Building ZINC001292588623 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588623 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 417) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n2n1) `ZINC001292588623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588623 none Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.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, 1, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 50, 50, 50, 36, 36, 36, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 418) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n2n1) `ZINC001292588623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292588623 none Cc1cc2nc(C)cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.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, 1, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 50, 50, 50, 36, 36, 36, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588623 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588623 Building ZINC001292588648 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588648 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/419 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(N)=O)c1) `ZINC001292588648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588648 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 11, 11, 11, 21, 21, 21, 21, 21, 44, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 11, 21, 21, 21, 44, 50, 50, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/420 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(N)=O)c1) `ZINC001292588648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588648 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 11, 11, 11, 21, 21, 21, 21, 21, 44, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 11, 21, 21, 21, 44, 50, 50, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588648 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 Building ZINC001292588648 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292588648 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 419) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(N)=O)c1) `ZINC001292588648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292588648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588648 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 11, 11, 11, 21, 21, 21, 21, 21, 44, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 11, 21, 21, 21, 44, 50, 50, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 420) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(N)=O)c1) `ZINC001292588648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292588648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292588648 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(NC(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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 11, 11, 11, 21, 21, 21, 21, 21, 44, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 11, 21, 21, 21, 44, 50, 50, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292588648 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292588648 Building ZINC001292593694 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593694 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/421 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1) `ZINC001292593694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593694 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 34, 34, 34, 44, 44, 44, 50, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 34, 44, 50, 50, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/422 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1) `ZINC001292593694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593694 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 33, 33, 33, 43, 43, 43, 50, 50, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 33, 43, 50, 50, 43] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593694 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 Building ZINC001292593694 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593694 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 421) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1) `ZINC001292593694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593694 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 34, 34, 34, 44, 44, 44, 50, 50, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 34, 44, 50, 50, 44] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 422) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1) `ZINC001292593694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593694 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cc(C(N)=O)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 33, 33, 33, 43, 43, 43, 50, 50, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 33, 43, 50, 50, 43] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593694 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593694 Building ZINC001292593715 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593715 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/423 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc21) `ZINC001292593715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001292593715 none Cn1nnc2cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 28, 28, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 28, 20, 20, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/424 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc21) `ZINC001292593715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001292593715 none Cn1nnc2cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 28, 28, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 28, 20, 20, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593715 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 Building ZINC001292593715 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593715 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 423) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc21) `ZINC001292593715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001292593715 none Cn1nnc2cc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 28, 28, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 28, 20, 20, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 424) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc21) `ZINC001292593715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001292593715 none Cn1nnc2cc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 28, 28, 28, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 28, 20, 20, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593715 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593715 Building ZINC001292593716 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593716 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/425 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21) `ZINC001292593716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593716 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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, 2, 8, 11, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 29, 50, 50, 50, 150] 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, 41, 42, 43]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/426 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21) `ZINC001292593716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593716 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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, 2, 8, 11, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 26, 50, 50, 50, 150] 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, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593716 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 Building ZINC001292593716 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593716 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 425) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21) `ZINC001292593716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593716 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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, 2, 8, 11, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 29, 50, 50, 50, 150] 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, 41, 42, 43]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 426) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21) `ZINC001292593716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292593716 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc2nc(O)[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 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, 2, 8, 11, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 26, 50, 50, 50, 150] 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, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593716 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593716 Building ZINC001292593731 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593731 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/427 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593731 none CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 50, 15, 15, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/428 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593731 none CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593731 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 Building ZINC001292593731 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593731 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 427) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593731 none CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 50, 15, 15, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 428) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593731 none CC(C)N1C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 24, 50, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593731 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593731 Building ZINC001292593733 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593733 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/429 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593733 none CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 22, 50, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/430 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593733 none CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 22, 50, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593733 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 Building ZINC001292593733 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292593733 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 429) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292593733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593733 none CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 22, 50, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 430) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001292593733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292593733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001292593733 none CC(C)N1C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 22, 50, 15, 15, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292593733 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292593733 Building ZINC001292594028 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594028 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/431 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1n1cccc1) `ZINC001292594028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001292594028 none Cn1ncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1n1cccc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/432 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1n1cccc1) `ZINC001292594028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001292594028 none Cn1ncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1n1cccc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594028 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 Building ZINC001292594028 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594028 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 431) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1n1cccc1) `ZINC001292594028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001292594028 none Cn1ncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1n1cccc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 432) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1n1cccc1) `ZINC001292594028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001292594028 none Cn1ncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1n1cccc1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 21, 21, 21, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594028 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594028 Building ZINC001292594034 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594034 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/433 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001292594034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594034 none Cn1cnc2cncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/434 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001292594034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594034 none Cn1cnc2cncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594034 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 Building ZINC001292594034 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594034 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 433) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001292594034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594034 none Cn1cnc2cncc(C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 434) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc2cncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001292594034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594034 none Cn1cnc2cncc(C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594034 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594034 Building ZINC001292594545 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594545 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/435 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1) `ZINC001292594545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292594545 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 22, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 47, 50, 50, 150] 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, 41, 42]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/436 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1) `ZINC001292594545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292594545 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 22, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 47, 50, 50, 150] 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, 41, 42]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594545 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 Building ZINC001292594545 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594545 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 435) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1) `ZINC001292594545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292594545 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 22, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 47, 50, 50, 150] 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, 41, 42]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 436) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1) `ZINC001292594545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001292594545 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1ccc2nc(O)[nH]c2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 8, 6, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 22, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 47, 50, 50, 150] 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, 41, 42]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594545 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594545 Building ZINC001292594562 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594562 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/437 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1) `ZINC001292594562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292594562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 12, 12, 12, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 12, 30, 30, 30, 50, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/438 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1) `ZINC001292594562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292594562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 13, 31, 31, 31, 50, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594562 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 Building ZINC001292594562 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594562 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 437) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1) `ZINC001292594562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292594562 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 12, 12, 12, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 12, 30, 30, 30, 50, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 438) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1) `ZINC001292594562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001292594562 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)c1cccc(c2nc[nH]n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 13, 13, 13, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 13, 31, 31, 31, 50, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594562 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594562 Building ZINC001292594598 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594598 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/439 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(N)=O)c1) `ZINC001292594598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594598 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 11, 20, 20, 20, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 20, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/440 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(N)=O)c1) `ZINC001292594598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594598 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 11, 20, 20, 20, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 20, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594598 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 Building ZINC001292594598 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594598 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 439) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(N)=O)c1) `ZINC001292594598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594598 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 11, 20, 20, 20, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 20, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 440) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(N)=O)c1) `ZINC001292594598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594598 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)COc1cccc(C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 11, 20, 20, 20, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 20, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594598 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594598 Building ZINC001292594645 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594645 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/441 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594645 none Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 50, 22, 22, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/442 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594645 none Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 22, 22, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594645 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 Building ZINC001292594645 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594645 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 441) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594645 none Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 50, 22, 22, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 442) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594645 none Cc1cn2c(n1)C[C@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 22, 22, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594645 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594645 Building ZINC001292594646 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594646 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/443 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594646 none Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 21, 21, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/444 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594646 none Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 50, 22, 22, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594646 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 Building ZINC001292594646 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594646 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 443) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594646 none Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 21, 21, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 444) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001292594646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001292594646 none Cc1cn2c(n1)C[C@@H](C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 50, 22, 22, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 22, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594646 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594646 Building ZINC001292594956 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594956 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/445 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292594956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594956 none Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 32, 41, 41, 32, 32, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 32, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/446 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292594956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594956 none Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 32, 39, 39, 32, 32, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 32, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 178 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594956 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 Building ZINC001292594956 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594956 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 445) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292594956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594956 none Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 32, 41, 41, 32, 32, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 32, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 446) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292594956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594956 none Cc1nn(C)c(C)c1[C@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 32, 39, 39, 32, 32, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 32, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 178 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594956 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594956 Building ZINC001292594957 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594957 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/447 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292594957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594957 none Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 32, 39, 39, 32, 32, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 32, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 178 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/448 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292594957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594957 none Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 32, 41, 41, 32, 32, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 32, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 184 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594957 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 Building ZINC001292594957 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594957 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 447) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001292594957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594957 none Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 32, 39, 39, 32, 32, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 32, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 178 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 448) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001292594957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001292594957 none Cc1nn(C)c(C)c1[C@@H](C)C(=O)NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 41, 32, 41, 41, 32, 32, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 32, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 184 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594957 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594957 Building ZINC001292594964 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594964 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/449 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21) `ZINC001292594964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594964 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 8, 20, 20, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/450 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21) `ZINC001292594964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594964 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594964 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 Building ZINC001292594964 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594964 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 449) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21) `ZINC001292594964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594964 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 8, 20, 20, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 450) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21) `ZINC001292594964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594964 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594964 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594964 Building ZINC001292594965 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594965 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/451 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21) `ZINC001292594965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594965 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/452 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21) `ZINC001292594965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594965 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 8, 20, 20, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594965 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 Building ZINC001292594965 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292594965 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 451) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21) `ZINC001292594965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292594965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594965 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 20, 20, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 452) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21) `ZINC001292594965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292594965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292594965 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)[C@H]1CNC(=O)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 8, 20, 20, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292594965 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292594965 Building ZINC001292595138 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292595138 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/453 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1) `ZINC001292595138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292595138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595138 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 30, 30, 30, 33, 33, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 14, 14, 30, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/454 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1) `ZINC001292595138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292595138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595138 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 24, 24, 24, 27, 27, 45, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 13, 13, 24, 27, 27, 27, 27, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292595138 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 Building ZINC001292595138 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292595138 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 453) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1) `ZINC001292595138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292595138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595138 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 30, 30, 30, 33, 33, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 14, 14, 30, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 454) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1) `ZINC001292595138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292595138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595138 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 24, 24, 24, 27, 27, 45, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 13, 13, 24, 27, 27, 27, 27, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292595138 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595138 Building ZINC001292595139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292595139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/455 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1) `ZINC001292595139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292595139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 23, 23, 23, 26, 26, 45, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 13, 13, 23, 26, 26, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/456 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1) `ZINC001292595139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292595139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 25, 25, 25, 31, 31, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 25, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292595139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 Building ZINC001292595139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292595139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 455) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1) `ZINC001292595139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292595139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 23, 23, 23, 26, 26, 45, 49, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 13, 13, 23, 26, 26, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 456) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1) `ZINC001292595139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292595139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001292595139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC(=O)CCOC[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 25, 25, 25, 31, 31, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 25, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292595139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292595139 Building ZINC001292900109 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292900109 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/457 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/457' -> `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)N1Cc2ccccc2C1) `ZINC001292900109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292900109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001292900109 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2C1 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.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 23, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 23, 23, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 91 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/458 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/458' -> `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)N1Cc2ccccc2C1) `ZINC001292900109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292900109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001292900109 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2C1 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.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 25, 25, 25, 7, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 93 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292900109 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 Building ZINC001292900109 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001292900109 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 457) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2C1) `ZINC001292900109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001292900109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001292900109 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1Cc2ccccc2C1 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.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 23, 23, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 23, 23, 6, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 91 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 458) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2C1) `ZINC001292900109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001292900109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001292900109 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1Cc2ccccc2C1 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.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 25, 25, 25, 7, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 93 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001292900109 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001292900109 Building ZINC001293203937 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293203937 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/459 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC2) `ZINC001293203937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293203937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293203937 none Cn1nc2c(c1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 46, 46, 34, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 33, 32, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/460 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC2) `ZINC001293203937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293203937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293203937 none Cn1nc2c(c1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 46, 46, 34, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 33, 32, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293203937 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 Building ZINC001293203937 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293203937 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 459) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC2) `ZINC001293203937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293203937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293203937 none Cn1nc2c(c1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 46, 46, 34, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 33, 32, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 460) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC2) `ZINC001293203937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293203937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293203937 none Cn1nc2c(c1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 46, 46, 34, 19, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 33, 32, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293203937 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293203937 Building ZINC001293204318 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204318 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/461 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21) `ZINC001293204318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204318 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 5, 5, 13, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 13, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/462 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21) `ZINC001293204318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204318 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 5, 5, 13, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 13, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204318 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 Building ZINC001293204318 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204318 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 461) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21) `ZINC001293204318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204318 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 5, 5, 13, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 13, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 462) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21) `ZINC001293204318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204318 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)Cn1ncc2cccnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 5, 5, 13, 13, 13, 29, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 13, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204318 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204318 Building ZINC001293204522 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204522 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/463 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001293204522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293204522 none CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 48, 48, 48, 48, 21, 21, 21, 13, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 21, 12, 13, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/464 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001293204522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293204522 none CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 48, 48, 48, 48, 22, 22, 22, 14, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 22, 13, 14, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204522 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 Building ZINC001293204522 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204522 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 463) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001293204522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293204522 none CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 48, 48, 48, 48, 21, 21, 21, 13, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 21, 12, 13, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 464) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001293204522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293204522 none CNC(=O)c1cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 48, 48, 48, 48, 22, 22, 22, 14, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 48, 48, 48, 22, 13, 14, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204522 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204522 Building ZINC001293204615 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204615 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/465 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=O) `ZINC001293204615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204615 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 21, 21, 21, 32, 32, 32, 32, 32, 47, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 13, 12, 21, 32, 32, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/466 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=O) `ZINC001293204615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204615 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 20, 20, 20, 32, 32, 32, 32, 32, 47, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 12, 13, 20, 32, 32, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204615 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 Building ZINC001293204615 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204615 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 465) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=O) `ZINC001293204615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204615 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 21, 21, 21, 32, 32, 32, 32, 32, 47, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 13, 12, 21, 32, 32, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 466) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=O) `ZINC001293204615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293204615 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccoc1CC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 20, 20, 20, 32, 32, 32, 32, 32, 47, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 12, 13, 20, 32, 32, 47, 47, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204615 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204615 Building ZINC001293204627 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204627 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/467 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc2c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn2c1) `ZINC001293204627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204627 none Cc1cnc2c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 31, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/468 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc2c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn2c1) `ZINC001293204627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204627 none Cc1cnc2c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 30, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204627 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 Building ZINC001293204627 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204627 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 467) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc2c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn2c1) `ZINC001293204627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204627 none Cc1cnc2c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 31, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 468) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnc2c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn2c1) `ZINC001293204627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204627 none Cc1cnc2c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 30, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204627 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204627 Building ZINC001293204660 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204660 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/469 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204660 none C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 42, 20, 20, 13, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 42, 42, 42, 20, 12, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/470 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204660 none C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 43, 22, 22, 13, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 22, 13, 12, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204660 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 Building ZINC001293204660 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204660 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 469) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204660 none C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 42, 20, 20, 13, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 42, 42, 42, 20, 12, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 470) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204660 none C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 43, 22, 22, 13, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 22, 13, 12, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204660 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204660 Building ZINC001293204661 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204661 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/471 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204661 none C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 17, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 27, 16, 16, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/472 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204661 none C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 48, 28, 28, 16, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 48, 48, 48, 28, 15, 14, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204661 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 Building ZINC001293204661 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204661 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 471) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204661 none C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 17, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 27, 16, 16, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 472) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204661 none C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 48, 28, 28, 16, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 48, 48, 48, 28, 15, 14, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204661 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204661 Building ZINC001293204663 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204663 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/473 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204663 none C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 43, 22, 22, 13, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 22, 12, 13, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/474 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204663 none C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 42, 20, 20, 13, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 42, 42, 42, 20, 12, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204663 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 Building ZINC001293204663 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204663 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 473) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204663 none C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 43, 22, 22, 13, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 22, 12, 13, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 474) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001293204663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204663 none C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 42, 20, 20, 13, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 42, 42, 42, 20, 12, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204663 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204663 Building ZINC001293204665 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204665 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/475 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204665 none C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 48, 28, 28, 16, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 48, 48, 48, 28, 14, 15, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/476 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204665 none C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 17, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 27, 15, 16, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204665 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 Building ZINC001293204665 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204665 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 475) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204665 none C[C@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 48, 28, 28, 16, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 48, 48, 48, 28, 14, 15, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 476) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001293204665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001293204665 none C[C@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 49, 27, 27, 17, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 27, 15, 16, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204665 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204665 Building ZINC001293204668 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204668 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/477 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293204668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001293204668 none Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 32, 32, 24, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 23, 23, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/478 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293204668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001293204668 none Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 31, 31, 24, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 23, 23, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204668 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 Building ZINC001293204668 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204668 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 477) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293204668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001293204668 none Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 32, 32, 24, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 23, 23, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 478) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293204668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001293204668 none Cn1cc(Cl)c(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 31, 31, 24, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 31, 23, 23, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204668 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204668 Building ZINC001293204903 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204903 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/479 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293204903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204903 none Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 41, 41, 41, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 41, 15, 16, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/480 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293204903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204903 none Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 41, 41, 41, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 41, 16, 15, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204903 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 Building ZINC001293204903 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204903 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 479) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293204903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204903 none Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 41, 41, 41, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 41, 15, 16, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 480) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293204903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204903 none Cc1csc(=O)n1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 41, 41, 41, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 41, 16, 15, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204903 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204903 Building ZINC001293204944 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204944 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/481 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001293204944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204944 none CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 42, 42, 42, 42, 20, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 42, 42, 42, 20, 20, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/482 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001293204944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204944 none CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 42, 42, 42, 42, 20, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 42, 42, 42, 20, 20, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204944 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 Building ZINC001293204944 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293204944 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 481) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001293204944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204944 none CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 42, 42, 42, 42, 20, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 42, 42, 42, 20, 20, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 482) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001293204944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293204944 none CC(=O)Nc1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 42, 42, 42, 42, 20, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50, 50, 42, 42, 42, 20, 20, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204944 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204944 Building ZINC001293204974 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293204974 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/483 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/484 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/485 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/485' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/486 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/486' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204974 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 Building ZINC001293204974 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293204974 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 483) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 484) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 485) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 486) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204974 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 Building ZINC001293204974 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293204974 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 483) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 484) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 485) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 486) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204974 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 Building ZINC001293204974 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293204974 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 483) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 484) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 14, 13, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 485) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 486) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C) `ZINC001293204974.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293204974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293204974 none C[C@H]1C[C@@H](C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 10, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 50, 20, 20, 14, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 13, 14, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293204974 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293204974 Building ZINC001293205038 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205038 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/487 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=O) `ZINC001293205038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205038 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 17, 31, 31, 35, 49, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 16, 17, 31, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/488 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=O) `ZINC001293205038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205038 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 17, 31, 31, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 16, 17, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205038 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 Building ZINC001293205038 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205038 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 487) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=O) `ZINC001293205038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205038 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 17, 31, 31, 35, 49, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 16, 17, 31, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 488) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=O) `ZINC001293205038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205038 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 17, 31, 31, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 16, 17, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205038 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205038 Building ZINC001293205039 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205039 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/489 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=O) `ZINC001293205039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205039 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 17, 33, 33, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 17, 16, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/490 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=O) `ZINC001293205039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205039 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 17, 31, 31, 35, 49, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 17, 16, 31, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205039 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 Building ZINC001293205039 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205039 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 489) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=O) `ZINC001293205039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205039 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 17, 33, 33, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 17, 16, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 490) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=O) `ZINC001293205039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205039 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@@H]1CCCCN1C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 17, 31, 31, 35, 49, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 17, 16, 31, 49, 49, 49, 49, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205039 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205039 Building ZINC001293205042 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205042 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/491 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1) `ZINC001293205042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 32, 32, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 15, 15, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/492 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1) `ZINC001293205042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 32, 32, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 15, 15, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205042 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 Building ZINC001293205042 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205042 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 491) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1) `ZINC001293205042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205042 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 32, 32, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 15, 15, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 492) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1) `ZINC001293205042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205042 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)C1(CF)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 32, 32, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 15, 15, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205042 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205042 Building ZINC001293205045 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205045 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/493 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1) `ZINC001293205045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205045 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 14, 21, 39, 39, 39, 48, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 21, 20, 39, 48, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/494 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1) `ZINC001293205045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205045 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 22, 39, 39, 39, 48, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 21, 22, 39, 48, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205045 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 Building ZINC001293205045 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205045 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 493) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1) `ZINC001293205045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205045 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 14, 21, 39, 39, 39, 48, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 15, 15, 21, 20, 39, 48, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 494) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1) `ZINC001293205045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205045 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 22, 39, 39, 39, 48, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 21, 22, 39, 48, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205045 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205045 Building ZINC001293205051 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205051 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/495 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205051 none COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 6, 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, 4, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 33, 33, 33, 24, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 50, 33, 24, 23, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/496 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205051 none COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 6, 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, 4, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 35, 35, 35, 25, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 50, 35, 25, 24, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205051 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 Building ZINC001293205051 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205051 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 495) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205051 none COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 6, 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, 4, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 33, 33, 33, 24, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 50, 33, 24, 23, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 496) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205051 none COc1cc(O)ncc1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 6, 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, 4, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 35, 35, 35, 25, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 50, 35, 25, 24, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205051 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205051 Building ZINC001293205062 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205062 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/497 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1) `ZINC001293205062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205062 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11, 16, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 15, 16, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/498 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1) `ZINC001293205062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205062 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11, 16, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 15, 16, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205062 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 Building ZINC001293205062 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205062 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 497) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1) `ZINC001293205062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205062 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11, 16, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 15, 16, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 498) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1) `ZINC001293205062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205062 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11, 16, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 15, 16, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205062 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205062 Building ZINC001293205226 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205226 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/499 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1) `ZINC001293205226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205226 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 9, 10, 18, 18, 18, 22, 39, 39, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 10, 9, 18, 22, 22, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/500 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1) `ZINC001293205226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205226 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 9, 10, 16, 16, 16, 20, 34, 34, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 9, 10, 16, 20, 20, 34, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205226 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 Building ZINC001293205226 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205226 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 499) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1) `ZINC001293205226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205226 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 9, 10, 18, 18, 18, 22, 39, 39, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 10, 9, 18, 22, 22, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 500) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1) `ZINC001293205226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205226 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)CNC(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 9, 10, 16, 16, 16, 20, 34, 34, 34, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 9, 10, 16, 20, 20, 34, 49, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205226 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205226 Building ZINC001293205179 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205179 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/501 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1) `ZINC001293205179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293205179 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 32, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 18, 18, 31, 31, 43, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/502 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1) `ZINC001293205179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293205179 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 31, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 30, 30, 42, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205179 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 Building ZINC001293205179 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205179 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 501) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1) `ZINC001293205179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293205179 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 32, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 18, 18, 31, 31, 43, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 502) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1) `ZINC001293205179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293205179 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1nnc2ccccc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 31, 42, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 30, 30, 42, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205179 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205179 Building ZINC001293205270 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293205270 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/503 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 10, 9, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/504 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 10, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 10, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/505 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/505' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 9, 10, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/506 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/506' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 7, 9, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205270 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 Building ZINC001293205270 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293205270 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 503) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 10, 9, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 504) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 10, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 10, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 505) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 9, 10, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 506) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 7, 9, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205270 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 Building ZINC001293205270 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293205270 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 503) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 10, 9, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 504) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 10, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 10, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 505) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 9, 10, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 506) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 7, 9, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205270 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 Building ZINC001293205270 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001293205270 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 503) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 10, 9, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 504) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 10, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 10, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 505) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 13, 38, 38, 38, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 9, 10, 10, 38, 38, 38, 38, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 506) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001293205270.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001293205270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293205270 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNC(=O)[C@H]1CC[C@@H](C(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 7, 9, 10, 10, 14, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 9, 10, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205270 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205270 Building ZINC001293205256 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205256 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/507 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205256 none CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 34, 34, 19, 11, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 18, 19, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/508 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205256 none CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 35, 35, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 17, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205256 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 Building ZINC001293205256 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205256 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 507) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205256 none CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 34, 34, 19, 11, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 18, 19, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 508) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205256 none CN1C(=O)CCC[C@@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 35, 35, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 17, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205256 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205256 Building ZINC001293205257 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205257 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/509 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205257 none CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 35, 35, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 17, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/510 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205257 none CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 50, 33, 33, 18, 11, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 18, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205257 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 Building ZINC001293205257 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205257 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 509) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205257 none CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 35, 35, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 17, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 510) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293205257 none CN1C(=O)CCC[C@H]1C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 50, 33, 33, 18, 11, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 18, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205257 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205257 Building ZINC001293205309 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205309 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/511 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001293205309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001293205309 none Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 16, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 14, 15, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/512 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001293205309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001293205309 none Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 14, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205309 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 Building ZINC001293205309 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205309 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 511) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001293205309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001293205309 none Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 16, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 14, 15, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 512) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21) `ZINC001293205309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001293205309 none Cn1nnc2cccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 31, 14, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205309 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205309 Building ZINC001293205384 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205384 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/513 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293205384 none Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 29, 42, 42, 29, 29, 17, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 29, 17, 16, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/514 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293205384 none Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 30, 45, 45, 30, 30, 17, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 30, 16, 17, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205384 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 Building ZINC001293205384 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205384 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 513) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293205384 none Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 29, 42, 42, 29, 29, 17, 10, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 29, 17, 16, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 514) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293205384 none Cn1cc(C(C)(C)C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 30, 45, 45, 30, 30, 17, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 30, 16, 17, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205384 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205384 Building ZINC001293205394 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205394 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/515 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293205394 none CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 25, 25, 25, 18, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 25, 18, 18, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/516 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293205394 none CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 24, 24, 24, 18, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 18, 18, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205394 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 Building ZINC001293205394 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205394 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 515) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293205394 none CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 25, 25, 25, 18, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 25, 18, 18, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 516) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001293205394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293205394 none CNC(=O)c1ccc(C(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 24, 24, 24, 18, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 24, 18, 18, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205394 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205394 Building ZINC001293205601 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205601 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/517 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293205601 none COc1ccncc1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 24, 24, 24, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 49, 49, 24, 16, 15, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/518 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293205601 none COc1ccncc1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 25, 25, 25, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 49, 49, 25, 16, 17, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205601 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 Building ZINC001293205601 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293205601 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 517) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001293205601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293205601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293205601 none COc1ccncc1CC(=O)NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 24, 24, 24, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 49, 49, 24, 16, 15, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 518) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001293205601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293205601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293205601 none COc1ccncc1CC(=O)NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input 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, 49, 25, 25, 25, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 49, 49, 25, 16, 17, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293205601 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293205601 Building ZINC001293516937 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293516937 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/519 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(C(=O)NCCCCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293516937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293516937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293516937 none Cn1nnc(C(=O)NCCCCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 19, 14, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 19, 19, 16, 16, 14, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/520 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(C(=O)NCCCCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293516937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293516937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293516937 none Cn1nnc(C(=O)NCCCCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 19, 14, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 19, 19, 16, 16, 16, 14, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293516937 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 Building ZINC001293516937 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293516937 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 519) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(C(=O)NCCCCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293516937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293516937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293516937 none Cn1nnc(C(=O)NCCCCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 19, 14, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 19, 19, 16, 16, 14, 16, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 520) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(C(=O)NCCCCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001293516937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293516937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293516937 none Cn1nnc(C(=O)NCCCCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 19, 14, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 32, 32, 19, 19, 16, 16, 16, 14, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293516937 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293516937 Building ZINC001293550758 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293550758 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/521 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293550758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293550758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293550758 none CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 17, 46, 46, 17, 17, 7, 7, 7, 7, 7, 4, 1, 6, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 17, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/522 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293550758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293550758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293550758 none CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 13, 41, 41, 13, 13, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293550758 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 Building ZINC001293550758 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293550758 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 521) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293550758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293550758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293550758 none CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 17, 46, 46, 17, 17, 7, 7, 7, 7, 7, 4, 1, 6, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 17, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 522) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293550758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293550758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293550758 none CNC(=O)NC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 13, 41, 41, 13, 13, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 41, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293550758 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293550758 Building ZINC001293551102 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551102 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/523 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1) `ZINC001293551102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 15, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 24, 24, 33, 33, 50, 50, 49, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49] set([38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/524 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1) `ZINC001293551102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 2, 2, 2, 2, 6, 6, 6, 25, 26, 46, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 25, 25, 35, 35, 40, 40, 50, 50, 49, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551102 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 Building ZINC001293551102 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551102 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 523) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1) `ZINC001293551102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 15, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 24, 24, 33, 33, 50, 50, 49, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49] set([38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 524) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1) `ZINC001293551102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 2, 2, 2, 2, 6, 6, 6, 25, 26, 46, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 6, 25, 25, 35, 35, 40, 40, 50, 50, 49, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551102 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551102 Building ZINC001293551167 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551167 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/525 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1) `ZINC001293551167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551167 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 24, 24, 24, 47, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 47, 47, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/526 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1) `ZINC001293551167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551167 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 15, 15, 15, 46, 50, 50, 50, 49, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 46, 46, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551167 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 Building ZINC001293551167 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551167 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 525) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1) `ZINC001293551167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551167 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 24, 24, 24, 47, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 47, 47, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 526) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1) `ZINC001293551167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551167 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 15, 15, 15, 46, 50, 50, 50, 49, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 46, 46, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551167 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551167 Building ZINC001293551773 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551773 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/527 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551773 none CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 50, 36, 37, 32, 8, 8, 8, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 37, 32, 32, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/528 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551773 none CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 50, 36, 37, 32, 10, 10, 10, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 37, 32, 32, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551773 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 Building ZINC001293551773 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551773 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 527) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551773 none CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 50, 36, 37, 32, 8, 8, 8, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 37, 32, 32, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 528) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551773 none CC[C@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 50, 36, 37, 32, 10, 10, 10, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 37, 32, 32, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551773 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551773 Building ZINC001293551774 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551774 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/529 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551774 none CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 38, 32, 9, 9, 9, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 38, 32, 32, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/530 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551774 none CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 50, 36, 37, 31, 7, 7, 7, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 37, 31, 31, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551774 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 Building ZINC001293551774 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551774 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 529) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551774 none CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 38, 32, 9, 9, 9, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 38, 32, 32, 9, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 530) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293551774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001293551774 none CC[C@@H](C)C(=O)NCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 50, 36, 37, 31, 7, 7, 7, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 37, 31, 31, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551774 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551774 Building ZINC001293551857 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551857 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/531 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001293551857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551857 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/532 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001293551857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551857 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 26, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 39, 39, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551857 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 Building ZINC001293551857 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551857 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 531) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001293551857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551857 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 35, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 532) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001293551857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551857 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 26, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 39, 39, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551857 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551857 Building ZINC001293551858 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551858 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/533 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001293551858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551858 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 18, 37, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/534 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001293551858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551858 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 17, 26, 37, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551858 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 Building ZINC001293551858 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551858 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 533) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001293551858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551858 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 18, 37, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 35, 35, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 534) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001293551858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551858 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 17, 26, 37, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551858 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551858 Building ZINC001293551901 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551901 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/535 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1) `ZINC001293551901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551901 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 7, 7, 7, 7, 7, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/536 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1) `ZINC001293551901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551901 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 6, 12, 12, 12, 37, 37, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551901 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 Building ZINC001293551901 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293551901 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 535) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1) `ZINC001293551901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293551901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551901 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 7, 7, 7, 7, 7, 14, 14, 14, 32, 32, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 536) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1) `ZINC001293551901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293551901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293551901 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCN2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.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, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 6, 12, 12, 12, 37, 37, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293551901 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293551901 Building ZINC001293569722 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293569722 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/537 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001293569722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293569722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293569722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 12, 12, 20, 21, 38, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 21, 21, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/538 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001293569722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293569722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293569722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 10, 10, 18, 19, 31, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 18, 18, 19, 19, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293569722 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 Building ZINC001293569722 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293569722 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 537) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001293569722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293569722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293569722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 12, 12, 20, 21, 38, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 21, 21, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 538) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001293569722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293569722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293569722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 10, 10, 18, 19, 31, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 18, 18, 19, 19, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293569722 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293569722 Building ZINC001293574843 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293574843 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/539 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1) `ZINC001293574843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293574843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293574843 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 24, 24, 24, 32, 32, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/540 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1) `ZINC001293574843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293574843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293574843 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 15, 15, 20, 20, 20, 26, 26, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293574843 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 Building ZINC001293574843 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293574843 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 539) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1) `ZINC001293574843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293574843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293574843 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 24, 24, 24, 32, 32, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 540) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1) `ZINC001293574843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293574843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293574843 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cn3c(n2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 15, 15, 20, 20, 20, 26, 26, 50, 50, 50, 50, 50, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293574843 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293574843 Building ZINC001293596656 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293596656 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/541 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001293596656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293596656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293596656 none COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 13, 20, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/542 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001293596656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293596656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293596656 none COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 12, 20, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293596656 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 Building ZINC001293596656 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293596656 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 541) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001293596656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293596656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293596656 none COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 13, 20, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 542) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001293596656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293596656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293596656 none COc1nccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 12, 20, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293596656 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293596656 Building ZINC001293605893 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293605893 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/543 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1) `ZINC001293605893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293605893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293605893 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 28, 28, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 150, 14, 14] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/544 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1) `ZINC001293605893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293605893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293605893 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 32, 32, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 150, 14, 14] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293605893 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 Building ZINC001293605893 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293605893 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 543) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1) `ZINC001293605893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293605893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293605893 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 28, 28, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 150, 14, 14] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 544) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1) `ZINC001293605893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293605893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293605893 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2csc(O)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 14, 1, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 32, 32, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 150, 14, 14] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293605893 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293605893 Building ZINC001293624911 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293624911 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/545 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001293624911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293624911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293624911 none COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 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', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 26, 12, 26, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/546 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001293624911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293624911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293624911 none COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 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', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 14, 27, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293624911 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 Building ZINC001293624911 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293624911 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 545) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001293624911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293624911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293624911 none COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 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', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 26, 12, 26, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 546) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001293624911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293624911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001293624911 none COc1ccc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 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', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 27, 14, 27, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293624911 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293624911 Building ZINC001293632936 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293632936 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/547 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293632936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632936 none COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 25, 11, 10, 11, 10, 10, 10, 4, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 38, 25, 25, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/548 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293632936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632936 none COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 22, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 38, 22, 22, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293632936 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 Building ZINC001293632936 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293632936 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 547) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293632936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632936 none COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 25, 11, 10, 11, 10, 10, 10, 4, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 38, 25, 25, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 548) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293632936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632936 none COC(=O)NCC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 22, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 38, 22, 22, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293632936 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632936 Building ZINC001293632937 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293632937 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/549 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293632937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632937 none COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 22, 8, 7, 8, 7, 7, 7, 3, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 39, 22, 22, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/550 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293632937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632937 none COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 25, 13, 11, 13, 11, 11, 11, 5, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 38, 25, 25, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293632937 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 Building ZINC001293632937 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293632937 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 549) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293632937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632937 none COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 22, 8, 7, 8, 7, 7, 7, 3, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 39, 22, 22, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 550) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293632937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293632937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293632937 none COC(=O)NCC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)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', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 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] dock color type numbers: [7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 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, 25, 13, 11, 13, 11, 11, 11, 5, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 38, 25, 25, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293632937 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293632937 Building ZINC001293641784 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293641784 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/551 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293641784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641784 none CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 11, 11, 23, 23, 23, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 23, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/552 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293641784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641784 none CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 22, 22, 22, 50, 50, 50, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293641784 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 Building ZINC001293641784 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293641784 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 551) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293641784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641784 none CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 11, 11, 23, 23, 23, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 23, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 552) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293641784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641784 none CN(C(=O)C(=O)NCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 22, 22, 22, 50, 50, 50, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293641784 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641784 Building ZINC001293641786 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293641786 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/553 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293641786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641786 none CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 7, 7, 20, 20, 20, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 20, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/554 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293641786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641786 none CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 23, 23, 23, 50, 50, 50, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 23, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293641786 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 Building ZINC001293641786 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293641786 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 553) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293641786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641786 none CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 7, 7, 20, 20, 20, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 20, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 554) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293641786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293641786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293641786 none CN(C(=O)C(=O)NCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 23, 23, 23, 50, 50, 50, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 23, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293641786 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293641786 Building ZINC001293642270 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642270 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/555 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642270 none CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 22, 22, 50, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 22, 22, 22, 22, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/556 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642270 none CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 22, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 22, 22, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642270 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 Building ZINC001293642270 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642270 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 555) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642270 none CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 22, 22, 50, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 22, 22, 22, 22, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 556) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642270 none CN(C(=O)CCc1nc[nH]n1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 22, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 22, 22, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642270 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642270 Building ZINC001293642271 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642271 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/557 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642271 none CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 21, 21, 50, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 21, 21, 21, 21, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/558 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642271 none CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 22, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 22, 22, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642271 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 Building ZINC001293642271 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642271 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 557) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642271 none CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 21, 21, 50, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 21, 21, 21, 21, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 558) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642271 none CN(C(=O)CCc1nc[nH]n1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 22, 22, 50, 50, 50, 50, 50, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 22, 22, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642271 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642271 Building ZINC001293642706 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642706 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/559 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/559' -> `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]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642706 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/560 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/560' -> `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]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642706 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 50, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642706 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 Building ZINC001293642706 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642706 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 559) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642706 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 560) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642706 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 50, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642706 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642706 Building ZINC001293642707 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642707 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/561 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/561' -> `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]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642707 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 28, 28, 50, 50, 50, 50, 50, 50, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/562 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/562' -> `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]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642707 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 14, 14, 14, 14, 14, 29, 29, 50, 50, 50, 50, 50, 50, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642707 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 Building ZINC001293642707 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642707 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 561) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642707 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 28, 28, 50, 50, 50, 50, 50, 50, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 562) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2nccnc2N)C1) `ZINC001293642707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293642707 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2nccnc2N)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 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] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 14, 14, 14, 14, 14, 29, 29, 50, 50, 50, 50, 50, 50, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642707 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642707 Building ZINC001293642812 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642812 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/563 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642812 none CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 26, 32, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 26, 26, 32, 32, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/564 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642812 none CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 26, 34, 50, 50, 50, 50, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 26, 26, 34, 34, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642812 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 Building ZINC001293642812 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642812 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 563) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642812 none CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 26, 32, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 26, 26, 32, 32, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 564) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642812 none CN(C(=O)CCn1cncn1)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 26, 34, 50, 50, 50, 50, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 26, 26, 34, 34, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642812 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642812 Building ZINC001293642813 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642813 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/565 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642813 none CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 26, 34, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 26, 26, 34, 34, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/566 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642813 none CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 26, 32, 50, 50, 50, 50, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 26, 26, 32, 32, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642813 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 Building ZINC001293642813 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293642813 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 565) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293642813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642813 none CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 26, 34, 50, 50, 50, 50, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 26, 26, 34, 34, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 566) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293642813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293642813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001293642813 none CN(C(=O)CCn1cncn1)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 26, 32, 50, 50, 50, 50, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 26, 26, 32, 32, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293642813 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293642813 Building ZINC001293643553 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293643553 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/567 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293643553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643553 none CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 6, 6, 19, 36, 50, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 19, 19, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/568 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293643553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643553 none CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 7, 7, 23, 40, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 23, 23, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293643553 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 Building ZINC001293643553 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293643553 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 567) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293643553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643553 none CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 6, 6, 19, 36, 50, 50, 50, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 19, 19, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 568) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293643553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643553 none CN(C(=O)COCC(F)F)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 7, 7, 23, 40, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 23, 23, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293643553 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643553 Building ZINC001293643554 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293643554 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/569 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293643554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643554 none CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 7, 7, 23, 40, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 23, 23, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/570 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293643554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643554 none CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 21, 37, 49, 50, 50, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 21, 21, 49, 49, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293643554 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 Building ZINC001293643554 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293643554 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 569) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293643554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643554 none CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 7, 7, 23, 40, 50, 50, 50, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 23, 23, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 570) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293643554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293643554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293643554 none CN(C(=O)COCC(F)F)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 21, 37, 49, 50, 50, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 21, 21, 49, 49, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293643554 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293643554 Building ZINC001293647129 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293647129 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/571 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/571' -> `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]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293647129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647129 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 8, 8, 8, 8, 8, 23, 23, 50, 50, 50, 50, 50, 50, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/572 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/572' -> `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]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293647129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647129 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 8, 8, 8, 8, 8, 23, 23, 50, 50, 50, 50, 50, 50, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293647129 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 Building ZINC001293647129 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293647129 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 571) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293647129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647129 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 8, 8, 8, 8, 8, 23, 23, 50, 50, 50, 50, 50, 50, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 572) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293647129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647129 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 8, 8, 8, 8, 8, 23, 23, 50, 50, 50, 50, 50, 50, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293647129 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647129 Building ZINC001293647130 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293647130 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/573 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/573' -> `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]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293647130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647130 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/574 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/574' -> `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]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293647130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647130 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293647130 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 Building ZINC001293647130 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293647130 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 573) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293647130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647130 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 574) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cnn(C)c2N)C1) `ZINC001293647130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293647130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293647130 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cnn(C)c2N)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 12, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293647130 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293647130 Building ZINC001293653882 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293653882 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/575 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/575' -> `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]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293653882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653882 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 7, 7, 21, 22, 50, 50, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 21, 21, 22, 22, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/576 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/576' -> `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]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293653882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653882 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 7, 7, 7, 7, 7, 8, 8, 20, 20, 50, 50, 50, 50, 50, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 20, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293653882 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 Building ZINC001293653882 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293653882 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 575) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293653882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653882 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 7, 7, 21, 22, 50, 50, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 21, 21, 22, 22, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 576) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293653882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653882 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 7, 7, 7, 7, 7, 8, 8, 20, 20, 50, 50, 50, 50, 50, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 20, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293653882 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653882 Building ZINC001293653883 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293653883 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/577 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/577' -> `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]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293653883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653883 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 7, 7, 7, 7, 7, 8, 8, 20, 21, 50, 50, 50, 50, 50, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 21, 21, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/578 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/578' -> `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]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293653883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653883 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 6, 6, 22, 23, 50, 50, 50, 50, 50, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 23, 23, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293653883 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 Building ZINC001293653883 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293653883 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 577) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293653883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653883 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 7, 7, 7, 7, 7, 8, 8, 20, 21, 50, 50, 50, 50, 50, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 21, 21, 50, 7, 7] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 578) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCc2nc[nH]n2)C1) `ZINC001293653883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293653883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293653883 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)CCc2nc[nH]n2)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 6, 6, 22, 23, 50, 50, 50, 50, 50, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 23, 23, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293653883 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293653883 Building ZINC001293661702 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293661702 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/579 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293661702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661702 none Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 11, 9, 11, 9, 9, 9, 4, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 37, 37, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/580 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293661702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661702 none Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 12, 10, 12, 10, 10, 10, 4, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 39, 39, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293661702 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 Building ZINC001293661702 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293661702 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 579) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293661702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661702 none Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 11, 9, 11, 9, 9, 9, 4, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 37, 37, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 580) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293661702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661702 none Cc1nccn1CC(=O)N1CC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 12, 10, 12, 10, 10, 10, 4, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 39, 39, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293661702 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661702 Building ZINC001293661703 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293661703 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/581 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293661703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661703 none Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 11, 10, 11, 10, 10, 10, 5, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 39, 39, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/582 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293661703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661703 none Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 10, 8, 10, 8, 8, 8, 4, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 37, 37, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293661703 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 Building ZINC001293661703 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293661703 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 581) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293661703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661703 none Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 11, 10, 11, 10, 10, 10, 5, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 39, 39, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 582) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293661703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293661703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293661703 none Cc1nccn1CC(=O)N1CC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 10, 8, 10, 8, 8, 8, 4, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 37, 37, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293661703 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293661703 Building ZINC001293676390 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293676390 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/583 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/583' -> `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]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293676390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676390 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 14, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 50, 50, 50, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/584 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/584' -> `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]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293676390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676390 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293676390 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 Building ZINC001293676390 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293676390 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 583) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293676390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676390 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 14, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 50, 50, 50, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 584) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293676390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676390 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293676390 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676390 Building ZINC001293676391 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293676391 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/585 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/585' -> `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]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293676391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676391 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 10, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/586 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/586' -> `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]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293676391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676391 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 14, 14, 14, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 50, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293676391 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 Building ZINC001293676391 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293676391 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 585) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293676391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676391 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 10, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 50, 50, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 586) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cc(=O)n(C)cn2)C1) `ZINC001293676391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293676391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293676391 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cc(=O)n(C)cn2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 14, 14, 14, 14, 14, 25, 25, 50, 50, 50, 50, 50, 50, 50, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293676391 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293676391 Building ZINC001293684815 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293684815 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/587 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/587' -> `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]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293684815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684815 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 18, 18, 18, 18, 31, 31, 50, 50, 50, 50, 50, 50, 50, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/588 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/588' -> `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]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293684815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684815 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 31, 31, 50, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293684815 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 Building ZINC001293684815 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293684815 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 587) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293684815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684815 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 18, 18, 18, 18, 18, 31, 31, 50, 50, 50, 50, 50, 50, 50, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 588) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293684815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684815 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 31, 31, 50, 50, 50, 50, 50, 50, 50, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293684815 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684815 Building ZINC001293684818 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293684818 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/589 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/589' -> `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]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293684818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684818 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 16, 16, 16, 16, 16, 32, 32, 50, 50, 50, 50, 50, 50, 50, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/590 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/590' -> `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]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293684818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684818 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 17, 17, 17, 17, 17, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293684818 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 Building ZINC001293684818 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293684818 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 589) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293684818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684818 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 16, 16, 16, 16, 16, 32, 32, 50, 50, 50, 50, 50, 50, 50, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 590) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cccn(C)c2=O)C1) `ZINC001293684818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293684818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293684818 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)c2cccn(C)c2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 17, 17, 17, 17, 17, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293684818 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293684818 Building ZINC001293687507 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293687507 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/591 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/591' -> `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]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293687507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687507 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 5, 5, 18, 37, 50, 50, 50, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 18, 50, 50, 50, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/592 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/592' -> `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]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293687507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687507 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 6, 6, 22, 42, 50, 50, 50, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293687507 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 Building ZINC001293687507 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293687507 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 591) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293687507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687507 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 5, 5, 18, 37, 50, 50, 50, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 18, 50, 50, 50, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 592) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293687507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687507 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 6, 6, 22, 42, 50, 50, 50, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293687507 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687507 Building ZINC001293687508 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293687508 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/593 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/593' -> `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]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293687508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687508 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 7, 7, 22, 41, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 22, 22, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/594 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/594' -> `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]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293687508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687508 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 5, 5, 18, 37, 50, 50, 50, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 18, 50, 50, 50, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293687508 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 Building ZINC001293687508 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293687508 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 593) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293687508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687508 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 7, 7, 22, 41, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 22, 22, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 594) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)COCC(F)F)C1) `ZINC001293687508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293687508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293687508 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)COCC(F)F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 5, 5, 18, 37, 50, 50, 50, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 18, 50, 50, 50, 4, 4] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293687508 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293687508 Building ZINC001293696663 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293696663 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/595 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/595' -> `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]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293696663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696663 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 18, 18, 18, 18, 18, 33, 39, 50, 50, 50, 50, 50, 50, 50, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/596 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/596' -> `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]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293696663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696663 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 32, 40, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293696663 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 Building ZINC001293696663 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293696663 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 595) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293696663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696663 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 18, 18, 18, 18, 18, 33, 39, 50, 50, 50, 50, 50, 50, 50, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 596) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293696663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696663 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 32, 40, 50, 50, 50, 50, 50, 50, 50, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293696663 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696663 Building ZINC001293696664 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293696664 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/597 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/597' -> `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]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293696664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696664 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 33, 37, 50, 50, 50, 50, 50, 50, 50, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/598 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/598' -> `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]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293696664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696664 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 18, 18, 18, 18, 18, 34, 36, 50, 50, 50, 50, 50, 50, 50, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293696664 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 Building ZINC001293696664 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293696664 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 597) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293696664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696664 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 33, 37, 50, 50, 50, 50, 50, 50, 50, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 598) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)C1) `ZINC001293696664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293696664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293696664 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CCC(=O)N2C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 18, 18, 18, 18, 18, 34, 36, 50, 50, 50, 50, 50, 50, 50, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 36, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293696664 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293696664 Building ZINC001293721117 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721117 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/599 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001293721117 none COCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 23, 12, 11, 12, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 44, 44, 23, 23, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/600 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001293721117 none COCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 23, 12, 11, 12, 11, 11, 11, 11, 11, 2, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 48, 48, 23, 23, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721117 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 Building ZINC001293721117 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721117 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 599) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001293721117 none COCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 23, 12, 11, 12, 11, 11, 11, 11, 10, 2, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 44, 44, 23, 23, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 600) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001293721117 none COCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 23, 12, 11, 12, 11, 11, 11, 11, 11, 2, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 48, 48, 23, 23, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721117 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721117 Building ZINC001293721139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/601 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721139 none CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 25, 35, 35, 50, 50, 50, 13, 25, 13, 13, 13, 13, 12, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/602 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721139 none CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 23, 36, 36, 50, 50, 50, 12, 23, 12, 12, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 307 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 Building ZINC001293721139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 601) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721139 none CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 25, 35, 35, 50, 50, 50, 13, 25, 13, 13, 13, 13, 12, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 602) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721139 none CC[C@@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 23, 36, 36, 50, 50, 50, 12, 23, 12, 12, 12, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 307 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721139 Building ZINC001293721141 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721141 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/603 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721141 none CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 25, 33, 33, 50, 50, 50, 12, 25, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 316 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/604 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721141 none CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 22, 34, 34, 50, 50, 50, 11, 22, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 315 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721141 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 Building ZINC001293721141 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721141 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 603) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721141 none CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 25, 33, 33, 50, 50, 50, 12, 25, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 316 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 604) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293721141 none CC[C@H](NC(C)=O)C(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 22, 34, 34, 50, 50, 50, 11, 22, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 315 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721141 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721141 Building ZINC001293721656 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721656 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/605 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293721656 none CCOCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', '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, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 36, 21, 12, 11, 12, 11, 11, 11, 11, 11, 2, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 47, 47, 21, 21, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/606 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293721656 none CCOCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', '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, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 18, 9, 8, 9, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 44, 44, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721656 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 Building ZINC001293721656 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293721656 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 605) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293721656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293721656 none CCOCCOCC(=O)N1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', '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, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 36, 21, 12, 11, 12, 11, 11, 11, 11, 11, 2, 10, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 47, 47, 21, 21, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 606) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293721656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293721656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293721656 none CCOCCOCC(=O)N1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', '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, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 18, 9, 8, 9, 8, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 44, 44, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293721656 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293721656 Building ZINC001293748276 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293748276 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/607 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1) `ZINC001293748276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293748276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293748276 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/608 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1) `ZINC001293748276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293748276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293748276 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293748276 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 Building ZINC001293748276 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293748276 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 607) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1) `ZINC001293748276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293748276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293748276 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 608) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1) `ZINC001293748276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293748276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293748276 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2cc[n+]([O-])cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293748276 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293748276 Building ZINC001293751750 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293751750 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/609 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1) `ZINC001293751750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293751750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293751750 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 22, 22, 25, 34, 34, 34, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 25, 25, 34, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/610 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1) `ZINC001293751750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293751750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293751750 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 21, 21, 22, 32, 32, 32, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 22, 22, 32, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293751750 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 Building ZINC001293751750 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293751750 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 609) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1) `ZINC001293751750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293751750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293751750 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 22, 22, 25, 34, 34, 34, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 25, 25, 34, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 610) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1) `ZINC001293751750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293751750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293751750 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)CNC(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 21, 21, 22, 32, 32, 32, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 11, 22, 22, 32, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293751750 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293751750 Building ZINC001293758302 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758302 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/611 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758302 none C[C@@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 34, 50, 9, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 34, 34, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/612 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758302 none C[C@@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 50, 6, 6, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 34, 34, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758302 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 Building ZINC001293758302 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758302 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 611) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758302 none C[C@@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 34, 50, 9, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 34, 34, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 612) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758302 none C[C@@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 34, 50, 6, 6, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 34, 34, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758302 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758302 Building ZINC001293758303 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758303 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/613 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758303 none C[C@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 49, 9, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 50, 50, 50, 49, 49, 49, 32, 32, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/614 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758303 none C[C@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 32, 50, 5, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 32, 32, 5, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758303 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 Building ZINC001293758303 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758303 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 613) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758303 none C[C@H](CC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 49, 9, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 50, 50, 50, 49, 49, 49, 32, 32, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50] 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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 614) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O) `ZINC001293758303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001293758303 none C[C@H](CC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 32, 50, 5, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 32, 32, 5, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758303 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758303 Building ZINC001293758468 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758468 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/615 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758468 none COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 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, 28, 21, 11, 21, 21, 11, 11, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 40, 40, 21, 21, 21, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/616 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758468 none COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 25, 18, 7, 18, 18, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 38, 38, 18, 18, 18, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758468 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 Building ZINC001293758468 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758468 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 615) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758468 none COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 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, 28, 21, 11, 21, 21, 11, 11, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 40, 40, 21, 21, 21, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 616) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758468 none COCCO[C@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 25, 18, 7, 18, 18, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 38, 38, 18, 18, 18, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758468 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758468 Building ZINC001293758469 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758469 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/617 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758469 none COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 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, 26, 21, 10, 21, 21, 10, 10, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 38, 38, 21, 21, 21, 10, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/618 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758469 none COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 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, 22, 18, 7, 18, 18, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 38, 38, 18, 18, 18, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758469 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 Building ZINC001293758469 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758469 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 617) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758469 none COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 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, 26, 21, 10, 21, 21, 10, 10, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 38, 38, 21, 21, 21, 10, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 618) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293758469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293758469 none COCCO[C@@H](C)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 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] 0 hydrogens need rotated 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, 22, 18, 7, 18, 18, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 38, 38, 18, 18, 18, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 49, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/13323/xbn-8058097.40/working/building/ZINC001293758469 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758469 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758469 Building ZINC001293758605 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758605 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/619 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=O)CC1) `ZINC001293758605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758605 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 8, 8, 27, 25, 45, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 27, 27, 33, 33, 40, 40, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/620 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=O)CC1) `ZINC001293758605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758605 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 10, 10, 10, 35, 29, 49, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 35, 35, 39, 39, 44, 43, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758605 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 Building ZINC001293758605 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758605 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 619) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=O)CC1) `ZINC001293758605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758605 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 8, 8, 27, 25, 45, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 8, 27, 27, 33, 33, 40, 40, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 620) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=O)CC1) `ZINC001293758605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758605 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCC(N)=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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 10, 10, 10, 35, 29, 49, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 35, 35, 39, 39, 44, 43, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758605 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758605 Building ZINC001293758999 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758999 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/621 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1) `ZINC001293758999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758999 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 7, 7, 7, 27, 24, 40, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 27, 27, 34, 34, 37, 36, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/622 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1) `ZINC001293758999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758999 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 2, 2, 2, 5, 5, 5, 31, 17, 42, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 31, 31, 32, 32, 37, 37, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758999 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 Building ZINC001293758999 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293758999 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 621) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1) `ZINC001293758999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293758999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758999 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 7, 7, 7, 27, 24, 40, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 27, 27, 34, 34, 37, 36, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 622) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1) `ZINC001293758999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293758999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293758999 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCn2ccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 2, 2, 2, 5, 5, 5, 31, 17, 42, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 31, 31, 32, 32, 37, 37, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293758999 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293758999 Building ZINC001293759027 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759027 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/623 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293759027 none CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'C.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, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 32, 11, 11, 11, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 44, 44, 32, 32, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/624 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293759027 none CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'C.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, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 32, 13, 13, 13, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 44, 44, 32, 32, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759027 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 Building ZINC001293759027 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759027 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 623) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293759027 none CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'C.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, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 32, 11, 11, 11, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 44, 44, 32, 32, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 624) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293759027 none CNC(=O)NCCC(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'C.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, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 32, 13, 13, 13, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 44, 44, 32, 32, 13, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759027 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759027 Building ZINC001293759488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/625 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1) `ZINC001293759488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759488 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/626 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1) `ZINC001293759488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759488 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 20, 20, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 Building ZINC001293759488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 625) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1) `ZINC001293759488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759488 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 626) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1) `ZINC001293759488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759488 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)C(=O)NCC(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 20, 20, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759488 Building ZINC001293759516 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759516 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/627 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=O)CC1) `ZINC001293759516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759516 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 1, 1, 2, 2, 2, 2, 4, 4, 4, 18, 24, 29, 46, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 18, 18, 29, 29, 29, 29, 46, 46, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/628 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=O)CC1) `ZINC001293759516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759516 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 1, 1, 2, 2, 2, 2, 6, 6, 6, 27, 30, 36, 47, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 27, 27, 36, 36, 36, 36, 47, 47, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759516 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 Building ZINC001293759516 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759516 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 627) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=O)CC1) `ZINC001293759516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759516 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 1, 1, 2, 2, 2, 2, 4, 4, 4, 18, 24, 29, 46, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 18, 18, 29, 29, 29, 29, 46, 46, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 628) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=O)CC1) `ZINC001293759516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293759516 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)CCCCC(N)=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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 8, 11, 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, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 1, 1, 2, 2, 2, 2, 6, 6, 6, 27, 30, 36, 47, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 27, 27, 36, 36, 36, 36, 47, 47, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759516 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759516 Building ZINC001293759756 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759756 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/629 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759756 none CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [41, 41, 9, 41, 41, 50, 50, 50, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 49, 49, 49, 49, 50, 50, 50, 50, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/630 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759756 none CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [42, 41, 11, 41, 41, 50, 50, 50, 11, 11, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 49, 49, 49, 49, 50, 50, 50, 50, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759756 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 Building ZINC001293759756 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759756 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 629) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759756 none CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [41, 41, 9, 41, 41, 50, 50, 50, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 49, 49, 49, 49, 50, 50, 50, 50, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 630) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759756 none CC[C@@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [42, 41, 11, 41, 41, 50, 50, 50, 11, 11, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 49, 49, 49, 49, 50, 50, 50, 50, 11, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759756 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759756 Building ZINC001293759757 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759757 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/631 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759757 none CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [42, 41, 9, 41, 41, 50, 50, 50, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/632 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759757 none CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [41, 43, 12, 43, 43, 50, 50, 50, 12, 12, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 49, 49, 49, 49, 50, 50, 50, 50, 12, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759757 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 Building ZINC001293759757 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293759757 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 631) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293759757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759757 none CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [42, 41, 9, 41, 41, 50, 50, 50, 9, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 632) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293759757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293759757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001293759757 none CC[C@H](NC(C)=O)C(=O)NC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 6, 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: [41, 43, 12, 43, 43, 50, 50, 50, 12, 12, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 49, 49, 49, 49, 49, 50, 50, 50, 50, 12, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293759757 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293759757 Building ZINC001293768156 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293768156 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/633 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(C(N)=O)c2)CC1) `ZINC001293768156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293768156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293768156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/634 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(C(N)=O)c2)CC1) `ZINC001293768156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293768156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293768156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293768156 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 Building ZINC001293768156 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293768156 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 633) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(C(N)=O)c2)CC1) `ZINC001293768156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293768156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293768156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 634) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(C(N)=O)c2)CC1) `ZINC001293768156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293768156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293768156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1CCN(C(=O)c2c[nH]c(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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293768156 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293768156 Building ZINC001293783309 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293783309 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/635 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293783309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293783309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293783309 none Cc1cncn1CC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 19, 7, 19, 7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 35, 35, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 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]) total number of confs: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/636 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293783309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293783309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293783309 none Cc1cncn1CC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 19, 7, 19, 7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 34, 34, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 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]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293783309 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 Building ZINC001293783309 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293783309 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 635) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293783309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293783309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293783309 none Cc1cncn1CC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 19, 7, 19, 7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 35, 35, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 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]) total number of confs: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 636) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293783309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293783309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293783309 none Cc1cncn1CC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 19, 7, 19, 7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 34, 34, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 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]) total number of confs: 155 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293783309 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293783309 Building ZINC001293803953 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293803953 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/637 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001293803953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293803953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293803953 none Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 28, 19, 7, 19, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 29, 29, 28, 28, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/638 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001293803953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293803953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293803953 none Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 25, 18, 8, 18, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 26, 26, 25, 25, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293803953 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 Building ZINC001293803953 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293803953 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 637) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001293803953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293803953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293803953 none Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 28, 19, 7, 19, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 29, 29, 28, 28, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 638) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001293803953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293803953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293803953 none Cn1ncc(CCC(=O)N2CCC(NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 25, 18, 8, 18, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 26, 26, 25, 25, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293803953 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293803953 Building ZINC001293812541 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293812541 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/639 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293812541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293812541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293812541 none COCCOCC(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 48, 33, 20, 20, 20, 20, 20, 20, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 49, 49, 33, 33, 20, 20, 20, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 50 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, 53]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/640 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293812541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293812541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293812541 none COCCOCC(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 20, 20, 20, 20, 20, 20, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 50 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, 53]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293812541 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 Building ZINC001293812541 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293812541 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 639) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293812541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293812541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293812541 none COCCOCC(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 48, 33, 20, 20, 20, 20, 20, 20, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 49, 49, 33, 33, 20, 20, 20, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 50 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, 53]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 640) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001293812541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293812541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293812541 none COCCOCC(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 20, 20, 20, 20, 20, 20, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 50, 50, 35, 35, 20, 20, 20, 20, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 50 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, 53]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293812541 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293812541 Building ZINC001293814037 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293814037 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/641 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=O)CC1) `ZINC001293814037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293814037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293814037 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 26, 26, 29, 29, 45, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 26, 26, 26, 26, 26, 45, 45, 50, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/642 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=O)CC1) `ZINC001293814037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293814037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293814037 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 27, 27, 27, 27, 31, 31, 47, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 27, 27, 27, 27, 27, 47, 47, 50, 50, 50, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293814037 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 Building ZINC001293814037 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293814037 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 641) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=O)CC1) `ZINC001293814037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293814037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293814037 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 26, 26, 29, 29, 45, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 26, 26, 26, 26, 26, 45, 45, 50, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 202 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 642) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=O)CC1) `ZINC001293814037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293814037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293814037 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CS(C)(=O)=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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 27, 27, 27, 27, 31, 31, 47, 50, 50, 50, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 27, 27, 27, 27, 27, 47, 47, 50, 50, 50, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293814037 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293814037 Building ZINC001293816843 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293816843 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/643 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1) `ZINC001293816843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293816843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816843 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 29, 29, 29, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 29, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 5, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/644 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1) `ZINC001293816843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293816843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816843 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 10, 29, 29, 29, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 29, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293816843 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 Building ZINC001293816843 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293816843 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 643) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1) `ZINC001293816843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293816843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816843 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 29, 29, 29, 50, 50, 50, 50, 50, 50, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 29, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 5, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 644) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1) `ZINC001293816843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293816843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816843 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(CNC(=O)Cc2cncnc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 10, 29, 29, 29, 50, 50, 50, 50, 50, 50, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 29, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293816843 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816843 Building ZINC001293816893 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293816893 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/645 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1) `ZINC001293816893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293816893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816893 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 28, 28, 28, 28, 29, 29, 29, 29, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 28, 28, 28, 28, 29, 29, 29, 29, 50, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/646 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1) `ZINC001293816893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293816893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816893 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 26, 26, 26, 26, 28, 28, 28, 28, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 26, 26, 26, 28, 28, 28, 28, 50, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293816893 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 Building ZINC001293816893 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293816893 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 645) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1) `ZINC001293816893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293816893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816893 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 28, 28, 28, 28, 29, 29, 29, 29, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 28, 28, 28, 28, 29, 29, 29, 29, 50, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 646) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1) `ZINC001293816893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293816893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293816893 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCc2nc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 26, 26, 26, 26, 28, 28, 28, 28, 50, 50, 50, 50, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 26, 26, 26, 26, 28, 28, 28, 28, 50, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293816893 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816893 Building ZINC001293816996 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293816996 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/647 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)NCC2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001293816996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293816996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293816996 none Cc1nc(CC(=O)NCC2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 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, 7, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 15, 15, 15, 9, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 33, 33, 15, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/648 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)NCC2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001293816996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293816996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293816996 none Cc1nc(CC(=O)NCC2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 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, 7, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 20, 20, 20, 6, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 37, 37, 20, 6, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 12, 13, 46, 15, 16, 17, 18, 19, 20, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293816996 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 Building ZINC001293816996 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293816996 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 647) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)NCC2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001293816996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293816996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293816996 none Cc1nc(CC(=O)NCC2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 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, 7, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 15, 15, 15, 9, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 33, 33, 15, 9, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 648) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CC(=O)NCC2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1) `ZINC001293816996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293816996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001293816996 none Cc1nc(CC(=O)NCC2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 8, 6, 7, 7, 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, 7, 6, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 20, 20, 20, 6, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 37, 37, 20, 6, 6, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 12, 13, 46, 15, 16, 17, 18, 19, 20, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293816996 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293816996 Building ZINC001293857307 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857307 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/649 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1) `ZINC001293857307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857307 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 10, 10, 10, 31, 18, 40, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 10, 31, 31, 31, 31, 37, 33, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/650 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1) `ZINC001293857307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857307 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 7, 7, 7, 27, 19, 42, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 27, 27, 31, 31, 37, 37, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857307 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 Building ZINC001293857307 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857307 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 649) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1) `ZINC001293857307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857307 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 10, 10, 10, 31, 18, 40, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 10, 31, 31, 31, 31, 37, 33, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 650) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1) `ZINC001293857307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857307 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 7, 7, 7, 27, 19, 42, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 27, 27, 31, 31, 37, 37, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857307 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857307 Building ZINC001293857360 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857360 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/651 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293857360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293857360 none CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 28, 7, 7, 7, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 30, 28, 28, 7, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/652 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293857360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293857360 none CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 29, 23, 5, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 29, 23, 23, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857360 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 Building ZINC001293857360 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857360 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 651) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293857360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293857360 none CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 28, 7, 7, 7, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 30, 28, 28, 7, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 652) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293857360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293857360 none CCCC(=O)NCC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 29, 23, 5, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 29, 23, 23, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857360 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857360 Building ZINC001293857793 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857793 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/653 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001293857793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857793 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 12, 12, 12, 36, 33, 49, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 36, 36, 41, 41, 46, 43, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/654 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001293857793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857793 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 4, 4, 6, 6, 6, 27, 28, 47, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 27, 27, 37, 37, 43, 42, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857793 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 Building ZINC001293857793 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857793 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 653) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001293857793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857793 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 12, 12, 12, 36, 33, 49, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 12, 36, 36, 41, 41, 46, 43, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 654) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1) `ZINC001293857793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857793 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 4, 4, 4, 6, 6, 6, 27, 28, 47, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 27, 27, 37, 37, 43, 42, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857793 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857793 Building ZINC001293857852 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857852 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/655 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1) `ZINC001293857852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857852 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 19, 19, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/656 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1) `ZINC001293857852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857852 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 3, 3, 3, 3, 3, 5, 5, 5, 18, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 18, 18, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857852 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 Building ZINC001293857852 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857852 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 655) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1) `ZINC001293857852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857852 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 7, 7, 7, 19, 48, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 19, 19, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 656) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1) `ZINC001293857852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857852 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 3, 3, 3, 3, 3, 5, 5, 5, 18, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 18, 18, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857852 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857852 Building ZINC001293857853 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857853 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/657 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1) `ZINC001293857853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857853 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 8, 8, 8, 18, 44, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 18, 18, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/658 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1) `ZINC001293857853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857853 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 7, 7, 7, 21, 48, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 7, 21, 21, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857853 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 Building ZINC001293857853 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293857853 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 657) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1) `ZINC001293857853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293857853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857853 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 8, 8, 8, 18, 44, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 18, 18, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 658) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1) `ZINC001293857853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293857853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293857853 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)CO[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 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, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 7, 7, 7, 21, 48, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 7, 21, 21, 50, 50, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293857853 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293857853 Building ZINC001293867122 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293867122 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/659 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001293867122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293867122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293867122 none Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 13, 8, 13, 8, 8, 8, 8, 5, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 152 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/660 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001293867122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293867122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293867122 none Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 11, 6, 11, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 30, 30, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 148 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293867122 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 Building ZINC001293867122 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293867122 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 659) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001293867122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293867122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293867122 none Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 13, 8, 13, 8, 8, 8, 8, 5, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 152 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 660) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1) `ZINC001293867122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293867122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001293867122 none Cc1nnc(CC(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 11, 6, 11, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 30, 30, 6, 6, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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]) total number of confs: 148 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293867122 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293867122 Building ZINC001293880862 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293880862 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/661 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001293880862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293880862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293880862 none CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 36, 20, 36, 20, 20, 20, 20, 6, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 42, 42, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 42, 42, 42, 42] 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]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/662 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001293880862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293880862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293880862 none CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 38, 19, 38, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 44, 44, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 44, 44, 44, 44] 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]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293880862 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 Building ZINC001293880862 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293880862 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 661) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001293880862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293880862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293880862 none CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 36, 20, 36, 20, 20, 20, 20, 6, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 42, 42, 50, 50, 50, 50, 20, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 42, 42, 42, 42] 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]) total number of confs: 155 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 662) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001293880862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293880862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001293880862 none CNC(=O)C1(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 38, 19, 38, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 44, 44, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 44, 44, 44, 44] 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]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293880862 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880862 Building ZINC001293880887 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293880887 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/663 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001293880887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293880887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293880887 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 25, 25, 25, 25, 25, 25, 34, 34, 37, 37, 37, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 25, 25, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/664 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001293880887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293880887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293880887 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 24, 34, 34, 37, 37, 37, 50, 50, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 24, 24, 37, 37, 37, 37, 37, 37, 50, 50, 24, 24] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293880887 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 Building ZINC001293880887 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293880887 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 663) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001293880887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293880887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293880887 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 25, 25, 25, 25, 25, 25, 34, 34, 37, 37, 37, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 25, 25, 25, 25, 25, 25, 37, 37, 37, 37, 37, 37, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 664) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001293880887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293880887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001293880887 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)C(C)(C)C(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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 24, 24, 24, 24, 24, 24, 34, 34, 37, 37, 37, 50, 50, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 24, 24, 24, 24, 24, 24, 37, 37, 37, 37, 37, 37, 50, 50, 24, 24] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293880887 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293880887 Building ZINC001293881524 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293881524 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/665 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293881524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293881524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293881524 none CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 26, 34, 34, 16, 26, 16, 16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 187 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/666 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293881524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293881524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293881524 none CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 27, 35, 35, 15, 27, 15, 15, 15, 15, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 187 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293881524 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 Building ZINC001293881524 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001293881524 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 665) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293881524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001293881524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293881524 none CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 26, 34, 34, 16, 26, 16, 16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 16, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 187 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 666) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001293881524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001293881524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001293881524 none CC(=O)NC(C)(C)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 27, 35, 35, 15, 27, 15, 15, 15, 15, 6, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 187 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001293881524 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001293881524 Building ZINC001294000417 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000417 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/667 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294000417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294000417 none CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 48, 34, 30, 34, 20, 30, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 48, 48, 30, 30, 30, 20, 20, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/668 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/668' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294000417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294000417 none CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 35, 32, 35, 21, 32, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 49, 32, 32, 32, 21, 21, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000417 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 Building ZINC001294000417 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000417 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 667) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294000417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294000417 none CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 48, 34, 30, 34, 20, 30, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 48, 48, 30, 30, 30, 20, 20, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 668) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294000417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294000417 none CCn1nnc(C)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 35, 32, 35, 21, 32, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 49, 32, 32, 32, 21, 21, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000417 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000417 Building ZINC001294000443 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000443 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/669 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12) `ZINC001294000443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000443 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 16, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/670 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12) `ZINC001294000443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000443 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 16, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000443 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 Building ZINC001294000443 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000443 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 669) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12) `ZINC001294000443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000443 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 16, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 670) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12) `ZINC001294000443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000443 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 16, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000443 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000443 Building ZINC001294000715 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000715 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/671 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n(C)n1) `ZINC001294000715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294000715 none Cc1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 22, 20, 22, 11, 20, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 20, 20, 20, 11, 11, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/672 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/672' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n(C)n1) `ZINC001294000715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294000715 none Cc1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 22, 20, 22, 11, 20, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 20, 20, 20, 11, 11, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000715 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 Building ZINC001294000715 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000715 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 671) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n(C)n1) `ZINC001294000715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294000715 none Cc1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 22, 20, 22, 11, 20, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 20, 20, 20, 11, 11, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 672) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n(C)n1) `ZINC001294000715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294000715 none Cc1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 22, 20, 22, 11, 20, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 20, 20, 20, 11, 11, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [48, 45, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/13323/xbn-8058097.40/working/building/ZINC001294000715 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000715 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000715 Building ZINC001294000725 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000725 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/673 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294000725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294000725 none Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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] 1 hydrogens 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, 33, 37, 21, 33, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 33, 33, 33, 20, 21, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/674 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294000725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294000725 none Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C 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', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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] 1 hydrogens 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, 38, 50, 50, 50, 38, 33, 38, 22, 33, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 33, 33, 33, 22, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000725 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 Building ZINC001294000725 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000725 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 673) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294000725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294000725 none Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C 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', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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] 1 hydrogens 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, 33, 37, 21, 33, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 33, 33, 33, 20, 21, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 674) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294000725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294000725 none Cc1ncnc(O)c1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C 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', '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'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 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] 1 hydrogens 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, 38, 50, 50, 50, 38, 33, 38, 22, 33, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 33, 33, 33, 22, 22, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 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]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000725 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000725 Building ZINC001294000729 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000729 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/675 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C) `ZINC001294000729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000729 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 20, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 43, 43, 50, 50, 50, 50, 50, 37, 37, 37, 20, 20, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/676 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C) `ZINC001294000729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000729 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 20, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 43, 43, 50, 50, 50, 50, 50, 37, 37, 37, 20, 20, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000729 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 Building ZINC001294000729 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000729 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 675) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C) `ZINC001294000729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000729 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 20, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 43, 43, 50, 50, 50, 50, 50, 37, 37, 37, 20, 20, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 676) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C) `ZINC001294000729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000729 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 20, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 43, 43, 50, 50, 50, 50, 50, 37, 37, 37, 20, 20, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000729 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000729 Building ZINC001294000747 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000747 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/677 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1) `ZINC001294000747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000747 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 15, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 15, 15, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/678 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1) `ZINC001294000747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000747 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 15, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 15, 15, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000747 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 Building ZINC001294000747 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000747 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 677) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1) `ZINC001294000747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000747 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 15, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 15, 15, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 678) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1) `ZINC001294000747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000747 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2ncccn2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 15, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 15, 15, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000747 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000747 Building ZINC001294000758 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000758 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/679 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001294000758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294000758 none COc1nccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 33, 27, 33, 17, 27, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 17, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/680 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001294000758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294000758 none COc1nccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 26, 34, 16, 26, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 26, 26, 26, 16, 15, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000758 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 Building ZINC001294000758 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000758 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 679) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001294000758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294000758 none COc1nccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 33, 27, 33, 17, 27, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 27, 27, 27, 16, 17, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 680) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001294000758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294000758 none COc1nccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 26, 34, 16, 26, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 26, 26, 26, 16, 15, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000758 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000758 Building ZINC001294000980 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000980 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/681 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000980 none CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 30, 12, 17, 8, 12, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 30, 30, 12, 12, 12, 8, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/682 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000980 none CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 23, 28, 11, 16, 7, 11, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 11, 11, 11, 7, 7, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000980 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 Building ZINC001294000980 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000980 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 681) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000980 none CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 30, 12, 17, 8, 12, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 50, 30, 30, 12, 12, 12, 8, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 682) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000980 none CCN1C[C@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 23, 28, 11, 16, 7, 11, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 11, 11, 11, 7, 7, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000980 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000980 Building ZINC001294000981 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000981 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/683 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000981 none CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 24, 28, 11, 16, 7, 11, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 11, 11, 11, 7, 7, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/684 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000981 none CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 25, 28, 12, 18, 8, 12, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 12, 12, 12, 8, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000981 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 Building ZINC001294000981 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000981 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 683) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000981.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000981 none CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 24, 28, 11, 16, 7, 11, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 11, 11, 11, 7, 7, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 684) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O) `ZINC001294000981.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294000981 none CCN1C[C@@H](C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 25, 28, 12, 18, 8, 12, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 12, 12, 12, 8, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000981 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000981 Building ZINC001294000989 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000989 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/685 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1) `ZINC001294000989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000989 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 29, 29, 31, 31, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/686 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1) `ZINC001294000989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000989 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 29, 29, 31, 31, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000989 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 Building ZINC001294000989 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294000989 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 685) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1) `ZINC001294000989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294000989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000989 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 29, 29, 31, 31, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 686) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1) `ZINC001294000989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294000989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294000989 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 29, 29, 31, 31, 50, 50, 50, 50, 50, 26, 26, 26, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294000989 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294000989 Building ZINC001294001097 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001097 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/687 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294001097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294001097 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 49, 40, 44, 25, 40, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 49, 49, 49, 49, 49, 49, 40, 40, 40, 25, 25, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/688 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294001097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294001097 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 49, 39, 43, 25, 39, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 49, 49, 49, 49, 49, 49, 39, 39, 39, 25, 25, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001097 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 Building ZINC001294001097 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001097 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 687) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294001097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294001097 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 49, 40, 44, 25, 40, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 49, 49, 49, 49, 49, 49, 40, 40, 40, 25, 25, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 688) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294001097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294001097 none CC(=O)N1CCC[C@@H]1C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 49, 39, 43, 25, 39, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 49, 49, 49, 49, 49, 49, 39, 39, 39, 25, 25, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001097 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001097 Building ZINC001294001100 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001100 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/689 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001294001100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001100 none COc1ccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 32, 43, 19, 32, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 18, 19, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/690 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001294001100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001100 none COc1ccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 33, 42, 20, 33, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 19, 19, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001100 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 Building ZINC001294001100 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001100 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 689) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001294001100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001100 none COc1ccc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 32, 43, 19, 32, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 18, 19, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 690) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001294001100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001100 none COc1ccc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 42, 33, 42, 20, 33, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 19, 19, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001100 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001100 Building ZINC001294001168 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001168 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/691 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1) `ZINC001294001168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001168 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 19, 19, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/692 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1) `ZINC001294001168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001168 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 18, 18, 18, 18, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001168 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 Building ZINC001294001168 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001168 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 691) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1) `ZINC001294001168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001168 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 19, 19, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 692) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1) `ZINC001294001168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001168 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 18, 18, 18, 18, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001168 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001168 Building ZINC001294001169 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001169 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/693 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1) `ZINC001294001169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001169 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 18, 18, 18, 18, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/694 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1) `ZINC001294001169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001169 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 19, 19, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001169 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 Building ZINC001294001169 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001169 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 693) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1) `ZINC001294001169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001169 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 18, 18, 18, 18, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 694) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1) `ZINC001294001169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001169 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCc2nncn2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 19, 19, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001169 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001169 Building ZINC001294001904 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001904 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/695 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294001904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001904 none CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 43, 43, 34, 27, 34, 14, 27, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 43, 43, 43, 27, 27, 27, 14, 14, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/696 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294001904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001904 none CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 30, 25, 30, 14, 25, 8, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 40, 40, 40, 25, 25, 25, 14, 14, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001904 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 Building ZINC001294001904 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001904 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 695) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294001904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001904 none CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 43, 43, 34, 27, 34, 14, 27, 9, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 43, 43, 43, 27, 27, 27, 14, 14, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 696) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294001904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294001904 none CC(=O)N1CC(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 30, 25, 30, 14, 25, 8, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 40, 40, 40, 25, 25, 25, 14, 14, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001904 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001904 Building ZINC001294001910 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001910 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/697 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2) `ZINC001294001910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001910 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 49, 49, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 14, 14, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/698 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2) `ZINC001294001910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001910 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 49, 49, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001910 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 Building ZINC001294001910 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294001910 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 697) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2) `ZINC001294001910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294001910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001910 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 49, 49, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 14, 14, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 698) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2) `ZINC001294001910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294001910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001294001910 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc2n(n1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 49, 49, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294001910 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294001910 Building ZINC001294185716 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294185716 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/699 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294185716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294185716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001294185716 none CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 7, 9, 16, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 16, 15, 20, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/700 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294185716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294185716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001294185716 none CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 7, 9, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 16, 17, 22, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294185716 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 Building ZINC001294185716 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294185716 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 699) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294185716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294185716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001294185716 none CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 7, 9, 16, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 16, 15, 20, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 700) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294185716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294185716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001294185716 none CN(CCCNC(=O)c1ccc2nnnn2c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 7, 9, 17, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 16, 17, 22, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294185716 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294185716 Building ZINC001294207813 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294207813 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/701 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001294207813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294207813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294207813 none COc1nc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 22, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 49, 22, 22, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/702 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001294207813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294207813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294207813 none COc1nc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 23, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 49, 23, 23, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294207813 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 Building ZINC001294207813 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294207813 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 701) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001294207813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294207813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294207813 none COc1nc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 22, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 49, 22, 22, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 702) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001294207813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294207813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294207813 none COc1nc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 23, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 50, 49, 23, 23, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294207813 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294207813 Building ZINC001294215300 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294215300 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/703 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294215300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294215300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294215300 none CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 22, 22, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/704 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294215300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294215300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294215300 none CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 22, 22, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294215300 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 Building ZINC001294215300 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294215300 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 703) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294215300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294215300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294215300 none CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 22, 22, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 704) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294215300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294215300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294215300 none CN(CCCNC(=O)c1ccnc2[nH]nnc21)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 22, 22, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294215300 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294215300 Building ZINC001294218669 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294218669 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/705 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294218669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294218669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294218669 none CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/706 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294218669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294218669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294218669 none CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294218669 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 Building ZINC001294218669 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294218669 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 705) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294218669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294218669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294218669 none CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 706) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294218669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294218669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294218669 none CN(CCCNC(=O)c1cccn(C)c1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294218669 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294218669 Building ZINC001294241170 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294241170 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/707 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294241170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294241170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294241170 none CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 13, 18, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 13, 13, 18, 18, 25, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/708 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294241170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294241170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294241170 none CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 12, 17, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 12, 12, 17, 17, 27, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294241170 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 Building ZINC001294241170 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294241170 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 707) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294241170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294241170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294241170 none CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 11, 13, 18, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 13, 13, 18, 18, 25, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 708) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294241170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294241170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294241170 none CN(CCCNC(=O)c1nccn2ccnc12)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 12, 17, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 12, 12, 17, 17, 27, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294241170 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294241170 Building ZINC001294242299 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294242299 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/709 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n2ncnc2n1) `ZINC001294242299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294242299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001294242299 none Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 29, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 43, 29, 29, 15, 15, 3, 3, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 184 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/710 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cccn2C)n2ncnc2n1) `ZINC001294242299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294242299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001294242299 none Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cccn2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 28, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 43, 28, 28, 15, 15, 3, 3, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294242299 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 Building ZINC001294242299 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294242299 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 709) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n2ncnc2n1) `ZINC001294242299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294242299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001294242299 none Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 29, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 43, 29, 29, 15, 15, 3, 3, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 184 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 710) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cccn2C)n2ncnc2n1) `ZINC001294242299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294242299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001294242299 none Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cccn2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 28, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 43, 28, 28, 15, 15, 3, 3, 3, 3, 3, 3, 3, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294242299 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294242299 Building ZINC001294314820 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294314820 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/711 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294314820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294314820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294314820 none CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 5, 7, 21, 21, 21, 45, 48, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 7, 7, 21, 45, 45, 48, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/712 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294314820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294314820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294314820 none CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 5, 7, 21, 21, 21, 44, 49, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 7, 7, 21, 44, 44, 49, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294314820 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 Building ZINC001294314820 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294314820 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 711) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294314820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294314820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294314820 none CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 5, 7, 21, 21, 21, 45, 48, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 7, 7, 21, 45, 45, 48, 48, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 712) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294314820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294314820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294314820 none CN(CCCNC(=O)CCc1cnccn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 5, 7, 21, 21, 21, 44, 49, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 7, 7, 21, 44, 44, 49, 49, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294314820 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294314820 Building ZINC001294320397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294320397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/713 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294320397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294320397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320397 none CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 18, 18, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/714 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/714' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294320397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294320397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320397 none CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 17, 18, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294320397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 Building ZINC001294320397 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294320397 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 713) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294320397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294320397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320397 none CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 18, 18, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 714) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294320397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294320397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320397 none CN(CCCNC(=O)[C@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 17, 18, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294320397 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320397 Building ZINC001294320398 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294320398 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/715 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294320398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320398 none CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 19, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 18, 19, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/716 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294320398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320398 none CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 18, 18, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294320398 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 Building ZINC001294320398 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294320398 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 715) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294320398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320398 none CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 19, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 18, 19, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 716) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294320398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294320398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294320398 none CN(CCCNC(=O)[C@@]1(C)CCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 42, 42, 43, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 18, 18, 42, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294320398 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294320398 Building ZINC001294390010 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294390010 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/717 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294390010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294390010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294390010 none CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 5, 5, 6, 11, 11, 11, 46, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 6, 6, 11, 46, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/718 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294390010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294390010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294390010 none CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 4, 4, 5, 11, 11, 11, 45, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 11, 45, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294390010 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 Building ZINC001294390010 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294390010 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 717) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294390010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294390010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294390010 none CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 5, 5, 6, 11, 11, 11, 46, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 6, 6, 11, 46, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 718) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294390010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294390010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294390010 none CCN(CCCNC(=O)CN1CCCC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 4, 4, 5, 11, 11, 11, 45, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 11, 45, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294390010 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294390010 Building ZINC001294410150 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410150 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/719 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410150 none CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 5, 12, 12, 12, 37, 37, 37, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 5, 5, 12, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/720 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410150 none CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 6, 14, 14, 14, 37, 37, 37, 37, 37, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 14, 37, 37, 50, 50, 50, 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410150 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 Building ZINC001294410150 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410150 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 719) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410150 none CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 5, 12, 12, 12, 37, 37, 37, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 5, 5, 12, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 720) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410150 none CCN(CCCNC(=O)[C@@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 6, 14, 14, 14, 37, 37, 37, 37, 37, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 14, 37, 37, 50, 50, 50, 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: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410150 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410150 Building ZINC001294410151 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410151 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/721 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410151 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 11, 11, 11, 36, 36, 36, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 11, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/722 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410151 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 4, 4, 5, 11, 11, 11, 37, 37, 37, 37, 37, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 11, 37, 37, 50, 50, 50, 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410151 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 Building ZINC001294410151 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410151 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 721) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410151 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 11, 11, 11, 36, 36, 36, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 11, 36, 36, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 722) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410151 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 4, 4, 5, 11, 11, 11, 37, 37, 37, 37, 37, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 11, 37, 37, 50, 50, 50, 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: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410151 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410151 Building ZINC001294410152 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410152 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/723 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410152 none CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 26, 26, 26, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/724 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410152 none CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 8, 8, 8, 25, 25, 25, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 8, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410152 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 Building ZINC001294410152 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410152 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 723) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410152 none CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 26, 26, 26, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 724) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410152 none CCN(CCCNC(=O)[C@H]1C[C@@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 8, 8, 8, 25, 25, 25, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 8, 25, 25, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410152 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410152 Building ZINC001294410153 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410153 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/725 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410153 none CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 26, 26, 26, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/726 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410153 none CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 8, 8, 8, 26, 26, 26, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 8, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410153 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 Building ZINC001294410153 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294410153 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 725) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294410153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294410153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410153 none CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 26, 26, 26, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 9, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 726) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294410153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294410153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001294410153 none CCN(CCCNC(=O)[C@@H]1C[C@H]1C(=O)OC)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 12, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 2, 3, 8, 8, 8, 26, 26, 26, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 8, 26, 26, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 2, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294410153 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294410153 Building ZINC001294412826 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412826 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/727 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/728 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/729 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/729' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/730 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/730' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412826 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 Building ZINC001294412826 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412826 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 727) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 728) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 729) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 730) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412826 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 Building ZINC001294412826 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412826 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 727) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 728) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 729) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 730) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412826 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 Building ZINC001294412826 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412826 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 727) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 728) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 729) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 17, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 40, 42, 44, 44, 44, 44, 44, 44, 33, 33, 33, 33, 33, 17, 17, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 730) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1) `ZINC001294412826.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412826 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 40, 40, 42, 42, 42, 42, 42, 42, 34, 34, 34, 34, 34, 17, 17, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412826 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412826 Building ZINC001294412827 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412827 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/731 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/732 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/733 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/733' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/734 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/734' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412827 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 Building ZINC001294412827 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412827 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 731) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 732) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 733) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 734) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412827 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 Building ZINC001294412827 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412827 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 731) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 732) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 733) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 734) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412827 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 Building ZINC001294412827 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294412827 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 731) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 732) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 733) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 38, 42, 42, 42, 42, 42, 42, 31, 31, 31, 31, 31, 16, 16, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 734) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1) `ZINC001294412827.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001294412827 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.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, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 39, 39, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412827 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412827 Building ZINC001294412908 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294412908 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/735 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1) `ZINC001294412908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294412908 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 13, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 26, 26, 43, 43, 43, 43, 43, 43, 29, 29, 29, 29, 29, 13, 13, 13, 13, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/736 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1) `ZINC001294412908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294412908 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 14, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 27, 31, 31, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 15, 15, 15, 15, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412908 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 Building ZINC001294412908 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294412908 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 735) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1) `ZINC001294412908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294412908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294412908 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 13, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 26, 26, 43, 43, 43, 43, 43, 43, 29, 29, 29, 29, 29, 13, 13, 13, 13, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 736) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1) `ZINC001294412908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294412908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294412908 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1(NC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 14, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 27, 31, 31, 44, 44, 44, 44, 44, 44, 32, 32, 32, 32, 32, 15, 15, 15, 15, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294412908 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294412908 Building ZINC001294413400 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294413400 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/737 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1) `ZINC001294413400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294413400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294413400 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 9, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 23, 23, 40, 40, 40, 40, 40, 40, 40, 22, 22, 22, 22, 22, 9, 9, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/738 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1) `ZINC001294413400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294413400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294413400 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 9, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 23, 23, 40, 40, 40, 40, 40, 40, 40, 22, 22, 22, 22, 22, 9, 9, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294413400 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 Building ZINC001294413400 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294413400 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 737) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1) `ZINC001294413400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294413400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294413400 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 9, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 23, 23, 40, 40, 40, 40, 40, 40, 40, 22, 22, 22, 22, 22, 9, 9, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 738) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1) `ZINC001294413400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294413400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001294413400 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 9, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 23, 23, 40, 40, 40, 40, 40, 40, 40, 22, 22, 22, 22, 22, 9, 9, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294413400 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413400 Building ZINC001294413637 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294413637 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/739 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001294413637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294413637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294413637 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 16, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 44, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 132] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 320 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/740 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001294413637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294413637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294413637 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 16, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 44, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 132] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 317 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294413637 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 Building ZINC001294413637 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294413637 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 739) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001294413637.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294413637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294413637 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 16, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 30, 30, 44, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 132] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 320 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 740) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1) `ZINC001294413637.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294413637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294413637 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)c(O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 22, 16, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 44, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 132] 150 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 317 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294413637 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294413637 Building ZINC001294414314 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294414314 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/741 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001294414314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294414314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294414314 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 16, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 39, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 16, 16, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/742 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001294414314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294414314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294414314 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 15, 12, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 39, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 15, 15, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294414314 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 Building ZINC001294414314 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294414314 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 741) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001294414314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294414314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294414314 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 16, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 39, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 16, 16, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 742) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1) `ZINC001294414314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294414314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294414314 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C1CS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 15, 12, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 39, 48, 48, 48, 48, 48, 28, 28, 28, 28, 28, 15, 15, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294414314 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294414314 Building ZINC001021423923 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001021423923 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/743 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001021423923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423923 none C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 40, 8, 23, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 40, 50, 50, 50, 50, 40, 40, 40, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/744 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001021423923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423923 none C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 8, 23, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 37, 50, 50, 50, 50, 37, 37, 37, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001021423923 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 Building ZINC001021423923 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001021423923 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 743) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001021423923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423923 none C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 40, 8, 23, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 40, 50, 50, 50, 50, 40, 40, 40, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 744) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001021423923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423923 none C[C@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 8, 23, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 37, 50, 50, 50, 50, 37, 37, 37, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001021423923 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423923 Building ZINC001021423925 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001021423925 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/745 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001021423925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423925 none C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 39, 7, 18, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 50, 50, 50, 50, 39, 39, 39, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/746 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001021423925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423925 none C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 36, 8, 17, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 36, 50, 50, 50, 50, 36, 36, 36, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001021423925 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 Building ZINC001021423925 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001021423925 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 745) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001021423925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423925 none C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 39, 7, 18, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 50, 50, 50, 50, 39, 39, 39, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 746) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1) `ZINC001021423925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001021423925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001021423925 none C[C@@H](C(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 36, 8, 17, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 36, 50, 50, 50, 50, 36, 36, 36, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001021423925 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001021423925 Building ZINC001294474101 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294474101 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/747 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294474101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294474101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474101 none CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 7, 8, 12, 27, 27, 32, 46, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 8, 8, 12, 12, 27, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/748 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294474101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294474101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474101 none CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 7, 8, 14, 30, 30, 34, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 8, 8, 14, 14, 30, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294474101 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 Building ZINC001294474101 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294474101 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 747) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294474101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294474101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474101 none CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 7, 8, 12, 27, 27, 32, 46, 46, 46, 46, 46, 46, 46, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 8, 8, 12, 12, 27, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 748) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294474101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294474101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474101 none CCN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 7, 8, 14, 30, 30, 34, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 8, 8, 14, 14, 30, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294474101 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474101 Building ZINC001294474102 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294474102 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/749 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294474102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294474102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474102 none CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 7, 8, 15, 37, 37, 40, 49, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 8, 8, 15, 15, 37, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/750 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294474102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294474102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474102 none CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 7, 8, 15, 37, 37, 40, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 8, 8, 15, 15, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294474102 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 Building ZINC001294474102 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294474102 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 749) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294474102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294474102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474102 none CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 7, 8, 15, 37, 37, 40, 49, 49, 49, 49, 49, 49, 49, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 8, 8, 15, 15, 37, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 750) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294474102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294474102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294474102 none CCN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 7, 8, 15, 37, 37, 40, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 8, 8, 15, 15, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294474102 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294474102 Building ZINC001294495762 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294495762 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/751 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294495762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294495762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294495762 none CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 11, 12, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 12, 12, 21, 21, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/752 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294495762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294495762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294495762 none CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 11, 12, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 12, 12, 20, 20, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294495762 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 Building ZINC001294495762 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294495762 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 751) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294495762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294495762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294495762 none CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 11, 12, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 12, 12, 21, 21, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 752) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294495762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294495762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294495762 none CCN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 11, 12, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 12, 12, 20, 20, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294495762 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294495762 Building ZINC001294504492 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294504492 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/753 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=O)CC1) `ZINC001294504492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294504492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001294504492 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=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.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 6, 14, 14, 14, 14, 35, 35, 35, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 35, 35, 35, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/754 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=O)CC1) `ZINC001294504492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294504492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001294504492 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=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.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 15, 15, 15, 15, 36, 36, 36, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 36, 36, 36, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294504492 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 Building ZINC001294504492 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294504492 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 753) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=O)CC1) `ZINC001294504492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294504492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001294504492 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=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.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 6, 14, 14, 14, 14, 35, 35, 35, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 35, 35, 35, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 754) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=O)CC1) `ZINC001294504492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294504492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001294504492 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(S(C)(=O)=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.3', 'C.3', 'C.3', 'S.o2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 15, 15, 15, 15, 36, 36, 36, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 36, 36, 36, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294504492 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294504492 Building ZINC001294517977 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294517977 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/755 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294517977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294517977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517977 none CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 9, 10, 15, 27, 27, 33, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 15, 15, 27, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/756 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/756' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294517977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294517977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517977 none CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 9, 10, 14, 27, 27, 33, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 14, 14, 27, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294517977 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 Building ZINC001294517977 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294517977 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 755) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294517977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294517977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517977 none CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 9, 10, 15, 27, 27, 33, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 15, 15, 27, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 756) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294517977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294517977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517977 none CCN(CCCNC(=O)[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 9, 10, 14, 27, 27, 33, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 14, 14, 27, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294517977 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517977 Building ZINC001294517978 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294517978 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/757 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294517978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294517978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517978 none CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 2, 7, 8, 9, 13, 27, 27, 33, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 13, 13, 27, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/758 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294517978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294517978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517978 none CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 9, 10, 16, 30, 30, 35, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 16, 16, 30, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294517978 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 Building ZINC001294517978 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294517978 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 757) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294517978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294517978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517978 none CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 2, 7, 8, 9, 13, 27, 27, 33, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 9, 9, 13, 13, 27, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 758) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294517978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294517978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294517978 none CCN(CCCNC(=O)[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 2, 7, 9, 10, 16, 30, 30, 35, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 10, 10, 16, 16, 30, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294517978 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294517978 Building ZINC001294542567 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294542567 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/759 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294542567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294542567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294542567 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 4, 4, 5, 13, 13, 13, 43, 43, 43, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 13, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [2, 49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/760 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294542567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294542567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294542567 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 6, 6, 7, 14, 14, 14, 43, 43, 43, 43, 43, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 14, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294542567 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 Building ZINC001294542567 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294542567 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 759) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001294542567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294542567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294542567 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 4, 4, 5, 13, 13, 13, 43, 43, 43, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 13, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [2, 49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 760) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001294542567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294542567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294542567 none CCN(CCCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 5, 6, 6, 7, 14, 14, 14, 43, 43, 43, 43, 43, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 14, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294542567 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294542567 Building ZINC001294552462 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294552462 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/761 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1) `ZINC001294552462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294552462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001294552462 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 4, 5, 19, 19, 5, 5, 5, 5, 13, 13, 13] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/762 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1) `ZINC001294552462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294552462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001294552462 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 4, 5, 20, 20, 5, 5, 5, 5, 12, 12, 12] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294552462 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 Building ZINC001294552462 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294552462 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 761) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1) `ZINC001294552462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294552462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001294552462 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 4, 5, 19, 19, 5, 5, 5, 5, 13, 13, 13] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 762) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1) `ZINC001294552462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294552462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001294552462 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 4, 5, 20, 20, 5, 5, 5, 5, 12, 12, 12] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294552462 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294552462 Building ZINC001294576620 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294576620 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/763 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1) `ZINC001294576620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294576620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 20, 29, 32, 43, 48, 48, 48, 48, 48, 48, 29, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 20, 20, 48, 48, 48, 48, 48, 48, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/764 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1) `ZINC001294576620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294576620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 21, 29, 33, 42, 48, 48, 48, 48, 48, 48, 29, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 21, 21, 48, 48, 48, 48, 48, 48, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294576620 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 Building ZINC001294576620 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294576620 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 763) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1) `ZINC001294576620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294576620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 20, 29, 32, 43, 48, 48, 48, 48, 48, 48, 29, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 20, 20, 48, 48, 48, 48, 48, 48, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 764) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1) `ZINC001294576620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294576620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 21, 29, 33, 42, 48, 48, 48, 48, 48, 48, 29, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 21, 21, 48, 48, 48, 48, 48, 48, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294576620 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576620 Building ZINC001294576621 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294576621 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/765 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1) `ZINC001294576621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294576621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576621 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 22, 32, 36, 42, 47, 47, 47, 47, 47, 47, 32, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 22, 22, 47, 47, 47, 47, 47, 47, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/766 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1) `ZINC001294576621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294576621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576621 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 21, 30, 33, 41, 46, 46, 46, 46, 46, 46, 30, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 21, 21, 46, 46, 46, 46, 46, 46, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294576621 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 Building ZINC001294576621 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294576621 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 765) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1) `ZINC001294576621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294576621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576621 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 22, 32, 36, 42, 47, 47, 47, 47, 47, 47, 32, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 22, 22, 47, 47, 47, 47, 47, 47, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 208 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 766) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1) `ZINC001294576621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294576621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576621 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)[C@@H]1COCCO1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 21, 30, 33, 41, 46, 46, 46, 46, 46, 46, 30, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 21, 21, 46, 46, 46, 46, 46, 46, 35, 35, 35, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294576621 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576621 Building ZINC001294576771 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294576771 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/767 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1) `ZINC001294576771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294576771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576771 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 20, 25, 25, 25, 31, 34, 50, 50, 50, 50, 25, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 20, 20, 31, 31, 34, 34, 50, 50, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/768 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1) `ZINC001294576771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294576771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576771 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 16, 22, 22, 22, 30, 35, 50, 50, 50, 50, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 12, 12, 16, 16, 30, 30, 35, 35, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294576771 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 Building ZINC001294576771 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294576771 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 767) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1) `ZINC001294576771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294576771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576771 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 20, 25, 25, 25, 31, 34, 50, 50, 50, 50, 25, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 20, 20, 31, 31, 34, 34, 50, 50, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 768) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1) `ZINC001294576771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294576771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294576771 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCn1cncn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 11, 16, 22, 22, 22, 30, 35, 50, 50, 50, 50, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 12, 12, 16, 16, 30, 30, 35, 35, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294576771 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294576771 Building ZINC001294577025 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294577025 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/769 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294577025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294577025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294577025 none CC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 47, 42, 38, 42, 23, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 43, 43, 49, 49, 49, 49, 47, 47, 23, 23, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/770 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294577025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294577025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294577025 none CC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 43, 37, 43, 24, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 45, 45, 48, 48, 48, 48, 45, 45, 24, 24, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294577025 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 Building ZINC001294577025 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294577025 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 769) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294577025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294577025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294577025 none CC(=O)NCC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 47, 42, 38, 42, 23, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 43, 43, 49, 49, 49, 49, 47, 47, 23, 23, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 770) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294577025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294577025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001294577025 none CC(=O)NCC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 45, 43, 37, 43, 24, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 45, 45, 48, 48, 48, 48, 45, 45, 24, 24, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294577025 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577025 Building ZINC001294577150 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294577150 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/771 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1) `ZINC001294577150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294577150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294577150 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 7, 9, 15, 22, 22, 22, 34, 38, 49, 49, 49, 49, 49, 22, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 15, 15, 34, 34, 38, 38, 49, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/772 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1) `ZINC001294577150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294577150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294577150 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 12, 19, 19, 19, 34, 37, 49, 49, 49, 49, 49, 19, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 12, 12, 34, 34, 37, 37, 49, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294577150 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 Building ZINC001294577150 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294577150 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 771) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1) `ZINC001294577150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294577150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294577150 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 7, 9, 15, 22, 22, 22, 34, 38, 49, 49, 49, 49, 49, 22, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 15, 15, 34, 34, 38, 38, 49, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 772) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1) `ZINC001294577150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294577150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294577150 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 12, 19, 19, 19, 34, 37, 49, 49, 49, 49, 49, 19, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 12, 12, 34, 34, 37, 37, 49, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294577150 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294577150 Building ZINC001294612754 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294612754 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/773 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001294612754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294612754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294612754 none Cn1ncc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 27, 11, 11, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 6, 6, 49, 49, 49, 49, 49, 49, 27, 26, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/774 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001294612754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294612754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294612754 none Cn1ncc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input 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, 26, 13, 11, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 50, 50, 50, 50, 50, 50, 26, 25, 14, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294612754 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 Building ZINC001294612754 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294612754 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 773) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001294612754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294612754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294612754 none Cn1ncc(C(=O)NCCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 27, 11, 11, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 6, 6, 49, 49, 49, 49, 49, 49, 27, 26, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 774) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001294612754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294612754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294612754 none Cn1ncc(C(=O)NCCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input 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, 26, 13, 11, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 6, 6, 50, 50, 50, 50, 50, 50, 26, 25, 14, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294612754 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294612754 Building ZINC001294654392 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294654392 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/775 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1) `ZINC001294654392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294654392 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 12, 23, 28, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 23, 23, 28, 28, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/776 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1) `ZINC001294654392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294654392 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 15, 15, 27, 27, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294654392 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 Building ZINC001294654392 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294654392 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 775) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1) `ZINC001294654392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294654392 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 12, 23, 28, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 23, 23, 28, 28, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 776) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1) `ZINC001294654392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294654392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294654392 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2cc[nH]n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 6, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 10, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 15, 15, 27, 27, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294654392 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294654392 Building ZINC001294658932 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294658932 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/777 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294658932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294658932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294658932 none C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 50, 30, 31, 30, 30, 30, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 30, 30, 30, 30, 14, 14, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/778 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294658932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294658932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294658932 none C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 50, 33, 35, 33, 33, 33, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 15, 14, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294658932 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 Building ZINC001294658932 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294658932 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 777) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294658932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294658932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294658932 none C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 50, 30, 31, 30, 30, 30, 16, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 30, 30, 30, 30, 14, 14, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 778) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294658932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294658932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294658932 none C[C@@H]1C[C@H]1C(=O)N1CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 50, 33, 35, 33, 33, 33, 17, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 15, 14, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294658932 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294658932 Building ZINC001294672038 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294672038 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/779 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1) `ZINC001294672038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294672038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294672038 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 12, 16, 35, 35, 35, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 16, 16, 35, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/780 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1) `ZINC001294672038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294672038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294672038 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 12, 32, 32, 32, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 12, 12, 32, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294672038 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 Building ZINC001294672038 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294672038 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 779) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1) `ZINC001294672038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294672038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294672038 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 12, 16, 35, 35, 35, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 16, 16, 35, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 780) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1) `ZINC001294672038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294672038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294672038 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)C(C)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 15, 15, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 12, 32, 32, 32, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 12, 12, 32, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294672038 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294672038 Building ZINC001294680035 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680035 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/781 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294680035 none CCCOCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 35, 27, 19, 27, 19, 19, 19, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 19, 19, 19, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/782 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294680035 none CCCOCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 30, 18, 30, 18, 18, 18, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 50, 50, 50, 50, 50, 50, 50, 36, 36, 18, 18, 18, 18, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680035 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 Building ZINC001294680035 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680035 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 781) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294680035 none CCCOCC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 35, 27, 19, 27, 19, 19, 19, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 50, 50, 50, 50, 50, 50, 50, 35, 35, 19, 19, 19, 19, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 782) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294680035 none CCCOCC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 30, 18, 30, 18, 18, 18, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 50, 50, 50, 50, 50, 50, 50, 36, 36, 18, 18, 18, 18, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680035 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680035 Building ZINC001294680055 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680055 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/783 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294680055 none Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 30, 39, 30, 30, 30, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 30, 30, 30, 30, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/784 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294680055 none Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 34, 45, 34, 34, 34, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 34, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680055 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 Building ZINC001294680055 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680055 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 783) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294680055 none Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 30, 39, 30, 30, 30, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 30, 30, 30, 30, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 784) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294680055 none Cc1c[nH]cc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 34, 45, 34, 34, 34, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 34, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680055 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680055 Building ZINC001294680626 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680626 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/785 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1) `ZINC001294680626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294680626 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 28, 39, 39, 39, 39, 39, 50, 50, 50, 50, 39, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/786 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1) `ZINC001294680626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294680626 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 29, 40, 40, 40, 40, 40, 50, 50, 50, 50, 40, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680626 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 Building ZINC001294680626 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680626 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 785) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1) `ZINC001294680626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294680626 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 28, 39, 39, 39, 39, 39, 50, 50, 50, 50, 39, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 39, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 786) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1) `ZINC001294680626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294680626 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)C=C2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 29, 40, 40, 40, 40, 40, 50, 50, 50, 50, 40, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680626 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680626 Building ZINC001294680717 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680717 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/787 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680717 none CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 18, 18, 18, 7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 39, 39, 18, 7, 7, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/788 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680717 none CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 19, 19, 19, 8, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 41, 41, 19, 8, 8, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680717 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 Building ZINC001294680717 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680717 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 787) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680717 none CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 18, 18, 18, 7, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 39, 39, 18, 7, 7, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 788) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680717 none CO[C@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 19, 19, 19, 8, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 41, 41, 19, 8, 8, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680717 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680717 Building ZINC001294680719 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680719 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/789 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680719 none CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 17, 17, 17, 7, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 39, 39, 17, 7, 7, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/790 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680719 none CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 21, 21, 21, 8, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 40, 40, 21, 8, 8, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 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/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680719 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 Building ZINC001294680719 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294680719 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 789) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294680719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680719 none CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 17, 17, 17, 7, 5, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 39, 39, 17, 7, 7, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 790) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001294680719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294680719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294680719 none CO[C@@H](C)CC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 21, 21, 21, 8, 5, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 40, 40, 21, 8, 8, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 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/13323/xbn-8058097.40/working/building/ZINC001294680719 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294680719 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294680719 Building ZINC001294688861 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294688861 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/791 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1) `ZINC001294688861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294688861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688861 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 10, 12, 24, 24, 24, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 12, 12, 24, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/792 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1) `ZINC001294688861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294688861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688861 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 11, 18, 18, 18, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 11, 11, 18, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294688861 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 Building ZINC001294688861 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294688861 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 791) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1) `ZINC001294688861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294688861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688861 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 10, 12, 24, 24, 24, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 12, 12, 24, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 792) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1) `ZINC001294688861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294688861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688861 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 11, 18, 18, 18, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 11, 11, 18, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294688861 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688861 Building ZINC001294688862 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294688862 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/793 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1) `ZINC001294688862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294688862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688862 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 10, 12, 23, 23, 23, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 12, 12, 23, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/794 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1) `ZINC001294688862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294688862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688862 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 7, 10, 19, 19, 19, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 10, 10, 19, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294688862 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 Building ZINC001294688862 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294688862 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 793) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1) `ZINC001294688862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294688862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688862 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 10, 12, 23, 23, 23, 50, 50, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 12, 12, 23, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 794) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1) `ZINC001294688862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294688862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294688862 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 7, 10, 19, 19, 19, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 10, 10, 19, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294688862 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294688862 Building ZINC001294715983 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294715983 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/795 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294715983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715983 none CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 26, 11, 8, 11, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 31, 29, 29, 26, 26, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/796 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294715983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715983 none CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 30, 31, 27, 12, 9, 12, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 31, 30, 30, 27, 27, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294715983 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 Building ZINC001294715983 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294715983 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 795) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294715983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715983 none CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 26, 11, 8, 11, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 31, 29, 29, 26, 26, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 796) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294715983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715983 none CCNC(=O)CCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 30, 31, 27, 12, 9, 12, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 31, 30, 30, 27, 27, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294715983 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715983 Building ZINC001294715985 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294715985 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/797 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294715985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715985 none CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 26, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 31, 29, 29, 26, 26, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/798 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294715985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715985 none CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 28, 30, 23, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 30, 28, 28, 23, 23, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294715985 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 Building ZINC001294715985 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294715985 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 797) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294715985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715985 none CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 26, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 31, 29, 29, 26, 26, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 798) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294715985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294715985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294715985 none CCNC(=O)CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 28, 30, 23, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 30, 28, 28, 23, 23, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294715985 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294715985 Building ZINC001294718863 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294718863 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/799 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294718863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718863 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 17, 17, 35, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 35, 35, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/800 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294718863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718863 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 33, 33, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294718863 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 Building ZINC001294718863 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294718863 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 799) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294718863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718863 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 17, 17, 35, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 35, 35, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 800) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294718863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718863 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 17, 17, 33, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 33, 33, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294718863 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718863 Building ZINC001294718864 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294718864 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/801 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294718864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718864 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 16, 16, 34, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 34, 34, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/802 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294718864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718864 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 14, 14, 36, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 36, 36, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294718864 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 Building ZINC001294718864 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294718864 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 801) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294718864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718864 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 16, 16, 34, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 34, 34, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 802) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1) `ZINC001294718864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294718864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294718864 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 14, 14, 36, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 36, 36, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294718864 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294718864 Building ZINC001294719616 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719616 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/803 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719616 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 18, 18, 18, 18, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/804 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719616 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 19, 19, 19, 19, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719616 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 Building ZINC001294719616 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719616 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 803) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719616 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 18, 18, 18, 18, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 804) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719616 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 19, 19, 19, 19, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719616 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719616 Building ZINC001294719620 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719620 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/805 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 21, 23, 23, 23, 23, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/806 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719620 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 Building ZINC001294719620 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719620 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 805) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 21, 23, 23, 23, 23, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 806) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1) `ZINC001294719620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nnnn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 19, 22, 22, 22, 22, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719620 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719620 Building ZINC001294719908 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719908 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/807 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719908 none C[C@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 36, 50, 50, 50, 50, 50, 36, 36, 36, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/808 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719908 none C[C@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 37, 12, 19, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 37, 50, 50, 50, 50, 50, 37, 37, 37, 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: [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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719908 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 Building ZINC001294719908 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719908 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 807) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719908 none C[C@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 36, 50, 50, 50, 50, 50, 36, 36, 36, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 808) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719908 none C[C@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 37, 12, 19, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 37, 50, 50, 50, 50, 50, 37, 37, 37, 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: [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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719908 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719908 Building ZINC001294719911 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719911 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/809 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719911 none C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 10, 18, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 32, 50, 50, 50, 50, 50, 32, 32, 32, 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: [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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/810 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719911 none C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 35, 14, 21, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 35, 50, 50, 50, 50, 50, 35, 35, 35, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719911 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 Building ZINC001294719911 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719911 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 809) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719911 none C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 10, 18, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 32, 50, 50, 50, 50, 50, 32, 32, 32, 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: [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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 810) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719911 none C[C@@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 35, 14, 21, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 35, 50, 50, 50, 50, 50, 35, 35, 35, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719911 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719911 Building ZINC001294719914 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719914 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/811 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719914 none C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 35, 12, 20, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 35, 50, 50, 50, 50, 50, 35, 35, 35, 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: [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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/812 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719914 none C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 38, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 38, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719914 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 Building ZINC001294719914 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719914 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 811) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719914 none C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 35, 12, 20, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 35, 50, 50, 50, 50, 50, 35, 35, 35, 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: [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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 812) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719914 none C[C@H](C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 38, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 38, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001294719914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719914 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719914 Building ZINC001294719916 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719916 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/813 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719916 none C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 34, 13, 18, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 34, 50, 50, 50, 50, 50, 34, 34, 34, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/814 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719916 none C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 13, 18, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 32, 50, 50, 50, 50, 50, 32, 32, 32, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719916 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 Building ZINC001294719916 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719916 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 813) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719916 none C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 34, 13, 18, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 34, 50, 50, 50, 50, 50, 34, 34, 34, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 814) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1) `ZINC001294719916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294719916 none C[C@@H](C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 13, 18, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 32, 50, 50, 50, 50, 50, 32, 32, 32, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001294719916 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719916 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719916 Building ZINC001294719989 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719989 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/815 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719989 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 13, 13, 20, 26, 26, 27, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 20, 20, 26, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/816 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719989 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 14, 14, 21, 25, 25, 26, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 21, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719989 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 Building ZINC001294719989 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719989 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 815) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719989 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 13, 13, 20, 26, 26, 27, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 20, 20, 26, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 816) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719989 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 14, 14, 21, 25, 25, 26, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 21, 21, 25, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719989 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719989 Building ZINC001294719991 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719991 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/817 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719991 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 9, 9, 9, 9, 9, 10, 10, 19, 23, 23, 23, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 19, 23, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/818 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719991 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 12, 12, 23, 29, 29, 29, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 23, 23, 29, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719991 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 Building ZINC001294719991 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294719991 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 817) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294719991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719991 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total 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, 9, 9, 9, 9, 9, 10, 10, 19, 23, 23, 23, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 19, 23, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 818) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1) `ZINC001294719991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294719991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294719991 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CNC(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 12, 12, 23, 29, 29, 29, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 23, 23, 29, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294719991 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294719991 Building ZINC001294720365 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720365 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/819 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 14, 14] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/820 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720365 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 Building ZINC001294720365 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720365 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 819) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720365 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 14, 14] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 820) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720365 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720365 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720365 Building ZINC001294720367 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720367 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/821 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720367 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/822 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720367 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720367 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 Building ZINC001294720367 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720367 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 821) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720367 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 822) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1) `ZINC001294720367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720367 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]cnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720367 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720367 Building ZINC001294720488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/823 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720488 none COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 25, 13, 25, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 100, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/824 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720488 none COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 29, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 100, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 Building ZINC001294720488 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720488 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 823) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720488 none COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 25, 13, 25, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 100, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 824) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720488 none COc1cc(O)ncc1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 29, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 100, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720488 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720488 Building ZINC001294720492 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720492 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/825 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720492 none COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 24, 12, 24, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 100, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/826 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720492 none COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 27, 14, 27, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 100, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720492 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 Building ZINC001294720492 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720492 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 825) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720492 none COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 24, 12, 24, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 100, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 826) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294720492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294720492 none COc1cc(O)ncc1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 50, 27, 14, 27, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 100, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 100 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720492 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720492 Building ZINC001294720907 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720907 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/827 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720907 none CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 28, 14, 12, 14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 28, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/828 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720907 none CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 29, 15, 12, 15, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 29, 50, 50, 50, 50, 50, 29, 29, 29, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720907 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 Building ZINC001294720907 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720907 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 827) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720907 none CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 28, 14, 12, 14, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 28, 50, 50, 50, 50, 50, 28, 28, 28, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 828) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720907 none CCn1nc(C)c(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 29, 15, 12, 15, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 29, 50, 50, 50, 50, 50, 29, 29, 29, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720907 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720907 Building ZINC001294720908 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720908 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/829 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720908 none CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 29, 17, 10, 17, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 29, 50, 50, 50, 50, 50, 29, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/830 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720908 none CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 28, 18, 13, 18, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 28, 50, 50, 50, 50, 50, 28, 28, 28, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720908 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 Building ZINC001294720908 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720908 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 829) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720908 none CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 29, 17, 10, 17, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 29, 50, 50, 50, 50, 50, 29, 29, 29, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 830) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001294720908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294720908 none CCn1nc(C)c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 28, 28, 18, 13, 18, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 28, 50, 50, 50, 50, 50, 28, 28, 28, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720908 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720908 Building ZINC001294720893 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720893 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/831 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720893 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 15, 15, 15, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/832 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720893 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 17, 17, 17, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720893 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 Building ZINC001294720893 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720893 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 831) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720893 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 15, 15, 15, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 832) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720893 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 17, 17, 17, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720893 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720893 Building ZINC001294720894 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720894 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/833 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720894 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 16, 16, 16, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/834 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720894 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 18, 18, 18, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720894 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 Building ZINC001294720894 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720894 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 833) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720894 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 16, 16, 16, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 834) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1) `ZINC001294720894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720894 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3ccncc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 18, 18, 18, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720894 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720894 Building ZINC001294720899 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720899 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/835 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720899 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 11, 11, 31, 31, 43, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 31, 31, 37, 37, 40, 41, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/836 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720899 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 9, 9, 28, 28, 42, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 28, 28, 35, 35, 40, 39, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720899 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 Building ZINC001294720899 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720899 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 835) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720899 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 11, 11, 31, 31, 43, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 31, 31, 37, 37, 40, 41, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 836) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720899 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 9, 9, 28, 28, 42, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 28, 28, 35, 35, 40, 39, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720899 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720899 Building ZINC001294720900 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720900 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/837 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720900 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 10, 10, 29, 31, 42, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 29, 29, 37, 37, 40, 40, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/838 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720900 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 12, 12, 29, 31, 43, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 29, 29, 37, 37, 39, 42, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720900 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 Building ZINC001294720900 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720900 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 837) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720900 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 10, 10, 29, 31, 42, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 29, 29, 37, 37, 40, 40, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 838) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1) `ZINC001294720900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294720900 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 12, 12, 29, 31, 43, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 29, 29, 37, 37, 39, 42, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720900 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720900 Building ZINC001294720910 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720910 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/839 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720910 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/840 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720910 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720910 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 Building ZINC001294720910 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720910 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 839) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720910 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 16, 16, 16, 16, 16, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 840) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720910 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 13, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720910 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720910 Building ZINC001294720911 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720911 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/841 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720911 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/842 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720911 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720911 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 Building ZINC001294720911 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294720911 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 841) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294720911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720911 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 842) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1) `ZINC001294720911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294720911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294720911 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294720911 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294720911 Building ZINC001294721458 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721458 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/843 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721458 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 8, 8, 23, 23, 28, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 23, 23, 28, 28, 28, 28, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/844 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721458 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 5, 5, 5, 5, 5, 7, 7, 19, 25, 27, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 19, 19, 27, 27, 27, 27, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721458 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 Building ZINC001294721458 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721458 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 843) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721458 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 8, 8, 23, 23, 28, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 23, 23, 28, 28, 28, 28, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 844) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721458 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 5, 5, 5, 5, 5, 7, 7, 19, 25, 27, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 19, 19, 27, 27, 27, 27, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721458 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721458 Building ZINC001294721460 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721460 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/845 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721460 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 6, 6, 6, 22, 22, 28, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 22, 22, 28, 28, 28, 28, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/846 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721460 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 24, 23, 28, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 24, 24, 28, 28, 28, 28, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721460 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 Building ZINC001294721460 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721460 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 845) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721460 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 6, 6, 6, 22, 22, 28, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 22, 22, 28, 28, 28, 28, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 846) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1) `ZINC001294721460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294721460 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 24, 23, 28, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 24, 24, 28, 28, 28, 28, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721460 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721460 Building ZINC001294721594 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721594 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/847 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721594 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/848 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721594 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 14, 14] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721594 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 Building ZINC001294721594 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721594 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 847) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721594 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 848) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721594 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 14, 14] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721594 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721594 Building ZINC001294721595 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721595 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/849 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721595 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/850 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721595 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721595 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 Building ZINC001294721595 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721595 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 849) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721595 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 850) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1) `ZINC001294721595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001294721595 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3[nH]ncc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721595 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721595 Building ZINC001294721597 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721597 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/851 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721597 none CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 27, 50, 15, 27, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/852 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721597 none CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 19, 31, 19, 19, 19, 4, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721597 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 Building ZINC001294721597 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721597 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 851) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721597 none CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 27, 50, 15, 27, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 852) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721597 none CN1C(=O)CCC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 19, 31, 19, 19, 19, 4, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721597 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721597 Building ZINC001294721600 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721600 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/853 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721600 none CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 16, 29, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/854 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721600 none CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 18, 31, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721600 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 Building ZINC001294721600 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294721600 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 853) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294721600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721600 none CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 16, 29, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 854) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294721600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294721600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001294721600 none CN1C(=O)CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 18, 31, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294721600 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294721600 Building ZINC001294722121 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722121 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/855 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722121 none CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 15, 19, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/856 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722121 none CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 15, 20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722121 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 Building ZINC001294722121 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722121 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 855) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722121 none CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 15, 19, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 856) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722121 none CN1CC[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 15, 20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722121 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722121 Building ZINC001294722108 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722108 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/857 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722108 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/858 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722108 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 16, 16, 16, 31, 31, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722108 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 Building ZINC001294722108 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722108 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 857) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722108 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 16, 16, 16, 33, 33, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 858) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722108 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 16, 16, 16, 31, 31, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722108 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722108 Building ZINC001294722111 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722111 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/859 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 32, 32, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/860 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 16, 16, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722111 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 Building ZINC001294722111 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722111 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 859) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 32, 32, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 860) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1) `ZINC001294722111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc(C(N)=O)o2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', '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: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of 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, 16, 16, 16, 16, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722111 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722111 Building ZINC001294722122 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722122 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/861 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722122 none CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 16, 50, 13, 16, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/862 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722122 none CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 14, 19, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 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]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722122 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 Building ZINC001294722122 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722122 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 861) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722122 none CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 16, 50, 13, 16, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 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]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 862) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722122 none CN1CC[C@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 14, 19, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 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]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722122 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722122 Building ZINC001294722124 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722124 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/863 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722124 none CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 14, 20, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 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]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/864 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722124 none CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 12, 19, 12, 12, 12, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 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]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722124 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 Building ZINC001294722124 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722124 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 863) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722124 none CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 14, 20, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 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]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 864) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722124 none CN1CC[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 19, 50, 12, 19, 12, 12, 12, 3, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 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]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722124 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722124 Building ZINC001294722126 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722126 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/865 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722126 none CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 15, 20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/866 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722126 none CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 50, 15, 22, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722126 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 Building ZINC001294722126 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722126 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 865) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722126 none CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 20, 50, 15, 20, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 866) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001294722126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294722126 none CN1CC[C@@H](C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 50, 15, 22, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722126 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722126 Building ZINC001294722399 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722399 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/867 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722399 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 14, 14, 33, 33, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 33, 33, 33, 33, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/868 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722399 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 9, 9, 9, 9, 13, 13, 34, 34, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722399 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 Building ZINC001294722399 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722399 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 867) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722399 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 14, 14, 33, 33, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 33, 33, 33, 33, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 868) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722399 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 9, 9, 9, 9, 9, 13, 13, 34, 34, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722399 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722399 Building ZINC001294722400 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722400 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/869 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722400 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 11, 11, 34, 34, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 34, 34, 34, 34, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/870 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722400 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 13, 13, 35, 35, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 35, 35, 35, 35, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722400 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 Building ZINC001294722400 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722400 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 869) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722400 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 11, 11, 34, 34, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 34, 34, 34, 34, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 870) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1) `ZINC001294722400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722400 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCc2cnccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 13, 13, 35, 35, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 35, 35, 35, 35, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722400 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722400 Building ZINC001294722918 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722918 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/871 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722918 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/872 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722918 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722918 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 Building ZINC001294722918 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722918 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 871) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722918 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 872) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722918 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722918 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722918 Building ZINC001294722919 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722919 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/873 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722919 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/874 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722919 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722919 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 Building ZINC001294722919 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294722919 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 873) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294722919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722919 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 874) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1) `ZINC001294722919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294722919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294722919 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccc3nn[nH]c3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294722919 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294722919 Building ZINC001294747875 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294747875 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/875 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1) `ZINC001294747875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294747875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294747875 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 19, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 27, 27, 34, 32, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49] set([38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/876 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1) `ZINC001294747875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294747875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294747875 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 15, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 25, 25, 34, 33, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49] set([38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294747875 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 Building ZINC001294747875 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294747875 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 875) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1) `ZINC001294747875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294747875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294747875 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 19, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 27, 27, 34, 32, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49] set([38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 876) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1) `ZINC001294747875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294747875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294747875 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCn2cccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 15, 39, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 25, 25, 34, 33, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49] set([38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294747875 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294747875 Building ZINC001294772032 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294772032 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/877 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294772032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 23, 23, 23, 43, 42, 42, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 23, 43, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/878 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294772032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 22, 22, 22, 41, 41, 41, 50, 50, 44, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 41, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294772032 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 Building ZINC001294772032 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294772032 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 877) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294772032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 23, 23, 23, 43, 42, 42, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 23, 43, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 878) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294772032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 22, 22, 22, 41, 41, 41, 50, 50, 44, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 41, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294772032 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772032 Building ZINC001294772033 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294772033 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/879 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294772033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772033 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 22, 22, 22, 47, 47, 47, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 47, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/880 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294772033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772033 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 21, 21, 21, 48, 48, 48, 50, 50, 48, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 48, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294772033 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 Building ZINC001294772033 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294772033 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 879) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294772033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772033 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 7, 22, 22, 22, 47, 47, 47, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 47, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 880) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001294772033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294772033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294772033 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 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, 4, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 21, 21, 21, 48, 48, 48, 50, 50, 48, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 48, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294772033 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294772033 Building ZINC001294775745 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294775745 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/881 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294775745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775745 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 27, 10, 27, 27, 10, 10, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 38, 38, 27, 27, 27, 27, 27, 27, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/882 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294775745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775745 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 33, 16, 33, 33, 16, 16, 9, 9, 9, 9, 9, 4, 1, 6, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 41, 41, 33, 33, 33, 33, 33, 33, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294775745 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 Building ZINC001294775745 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294775745 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 881) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294775745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775745 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 27, 10, 27, 27, 10, 10, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 38, 38, 27, 27, 27, 27, 27, 27, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 882) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294775745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775745 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 33, 16, 33, 33, 16, 16, 9, 9, 9, 9, 9, 4, 1, 6, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 41, 41, 33, 33, 33, 33, 33, 33, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294775745 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775745 Building ZINC001294775746 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294775746 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/883 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294775746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775746 none CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 33, 16, 33, 33, 16, 16, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 40, 40, 33, 33, 33, 33, 33, 33, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/884 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294775746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775746 none CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 30, 12, 30, 30, 12, 12, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 41, 41, 30, 30, 30, 30, 30, 30, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294775746 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 Building ZINC001294775746 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294775746 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 883) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294775746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775746 none CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 33, 16, 33, 33, 16, 16, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 40, 40, 33, 33, 33, 33, 33, 33, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 884) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001294775746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294775746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001294775746 none CC(=O)NCC(C)(C)C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 30, 12, 30, 30, 12, 12, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 41, 41, 30, 30, 30, 30, 30, 30, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294775746 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294775746 Building ZINC001294813207 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294813207 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/885 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294813207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813207 none CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 21, 50, 21, 21, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/886 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294813207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813207 none CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 22, 50, 22, 22, 10, 10, 10, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294813207 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 Building ZINC001294813207 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294813207 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 885) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294813207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813207 none CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 21, 50, 21, 21, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 886) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294813207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813207 none CC(C)[C@H](C(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 22, 50, 22, 22, 10, 10, 10, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294813207 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813207 Building ZINC001294813206 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294813206 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/887 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294813206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813206 none CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 38, 18, 47, 18, 18, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 1, 1, 1, 8, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/888 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294813206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813206 none CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 36, 21, 49, 21, 21, 10, 10, 10, 10, 10, 4, 1, 8, 1, 1, 1, 1, 1, 1, 10, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 286 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294813206 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 Building ZINC001294813206 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294813206 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 887) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294813206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813206 none CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 38, 18, 47, 18, 18, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 1, 1, 1, 8, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 888) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001294813206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294813206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294813206 none CC(C)[C@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 36, 21, 49, 21, 21, 10, 10, 10, 10, 10, 4, 1, 8, 1, 1, 1, 1, 1, 1, 10, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 286 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294813206 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294813206 Building ZINC001294853711 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294853711 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/889 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294853711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853711 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 24, 48, 48, 48, 50, 50, 48, 48, 50, 50, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 48, 50, 50, 50, 50, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/890 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294853711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853711 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 26, 44, 44, 44, 45, 45, 44, 44, 45, 45, 10, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 44, 45, 45, 45, 45, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294853711 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 Building ZINC001294853711 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294853711 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 889) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294853711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853711 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 24, 48, 48, 48, 50, 50, 48, 48, 50, 50, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 48, 50, 50, 50, 50, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 890) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294853711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853711 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 26, 44, 44, 44, 45, 45, 44, 44, 45, 45, 10, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 26, 26, 44, 45, 45, 45, 45, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294853711 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853711 Building ZINC001294853712 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294853712 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/891 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294853712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853712 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 27, 43, 43, 43, 45, 45, 45, 45, 45, 45, 10, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 43, 45, 45, 45, 45, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/892 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294853712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853712 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 48, 50, 50, 50, 50, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294853712 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 Building ZINC001294853712 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294853712 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 891) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294853712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853712 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 10, 27, 43, 43, 43, 45, 45, 45, 45, 45, 45, 10, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 27, 27, 43, 45, 45, 45, 45, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 892) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1) `ZINC001294853712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294853712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294853712 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)c1cc[n+]([O-])cc1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 24, 48, 48, 48, 50, 50, 50, 50, 50, 50, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 24, 24, 48, 50, 50, 50, 50, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294853712 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294853712 Building ZINC001294865914 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294865914 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/893 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294865914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865914 none Cc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 46, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 50, 50, 50, 50, 50, 50, 50, 46, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/894 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294865914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865914 none Cc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 46, 23, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 50, 50, 46, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294865914 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 Building ZINC001294865914 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294865914 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 893) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294865914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865914 none Cc1cc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 46, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 50, 50, 50, 50, 50, 50, 50, 46, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 894) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294865914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865914 none Cc1cc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 46, 23, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 50, 50, 46, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294865914 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865914 Building ZINC001294865915 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294865915 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/895 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294865915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865915 none Cc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 46, 24, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 50, 50, 50, 50, 50, 50, 50, 46, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/896 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294865915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865915 none Cc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 14, 14, 49, 49, 49, 49, 49, 49, 49, 46, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 49, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294865915 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 Building ZINC001294865915 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294865915 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 895) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294865915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865915 none Cc1cc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 46, 46, 24, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 50, 50, 50, 50, 50, 50, 50, 46, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 896) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1) `ZINC001294865915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294865915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294865915 none Cc1cc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n(C)n1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 46, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 14, 14, 49, 49, 49, 49, 49, 49, 49, 46, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 49, 49, 49] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294865915 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294865915 Building ZINC001294866445 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866445 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/897 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866445 none CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 25, 20, 20, 20, 9, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 41, 25, 25, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/898 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866445 none CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 26, 23, 23, 23, 9, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 40, 26, 26, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866445 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 Building ZINC001294866445 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866445 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 897) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866445 none CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 25, 20, 20, 20, 9, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 41, 25, 25, 20, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 898) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866445 none CCC(=O)NCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 26, 23, 23, 23, 9, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 40, 26, 26, 23, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866445 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866445 Building ZINC001294866446 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866446 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/899 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866446 none CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 24, 22, 22, 22, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 42, 24, 24, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/900 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866446 none CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 25, 21, 21, 21, 11, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 40, 25, 25, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866446 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 Building ZINC001294866446 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866446 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 899) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866446 none CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 24, 22, 22, 22, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 42, 24, 24, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 900) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294866446 none CCC(=O)NCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 25, 21, 21, 21, 11, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 40, 25, 25, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866446 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866446 Building ZINC001294866792 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866792 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/901 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866792 none Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 33, 33, 49, 49, 49, 49, 49, 49, 49, 40, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33] 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: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/902 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866792 none Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 41, 41, 49, 49, 49, 49, 49, 49, 49, 45, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 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: 220 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866792 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 Building ZINC001294866792 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866792 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 901) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866792 none Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 40, 25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 33, 33, 49, 49, 49, 49, 49, 49, 49, 40, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33] 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: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 902) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866792 none Cc1nn(C)cc1C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 41, 41, 49, 49, 49, 49, 49, 49, 49, 45, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 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: 220 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866792 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866792 Building ZINC001294866793 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866793 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/903 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866793 none Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 41, 41, 49, 49, 49, 49, 49, 49, 49, 45, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 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: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/904 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866793 none Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 48, 48, 48, 48, 48, 48, 48, 43, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 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: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866793 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 Building ZINC001294866793 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866793 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 903) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866793 none Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 41, 41, 49, 49, 49, 49, 49, 49, 49, 45, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 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: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 904) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866793 none Cc1nn(C)cc1C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 48, 48, 48, 48, 48, 48, 48, 43, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 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: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866793 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866793 Building ZINC001294866827 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866827 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/905 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866827 none Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 15, 15, 15, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 50, 50, 50, 50, 50, 40, 40, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/906 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866827 none Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 12, 8, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 38, 38, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866827 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 Building ZINC001294866827 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866827 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 905) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866827 none Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 15, 15, 15, 7, 5, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 50, 50, 50, 50, 50, 40, 40, 15, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 906) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866827 none Cc1cncn1CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 16, 16, 16, 12, 8, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 38, 38, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866827 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866827 Building ZINC001294866834 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866834 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/907 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866834 none Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 16, 16, 16, 10, 8, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 37, 37, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/908 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866834 none Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 16, 16, 16, 6, 4, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 35, 35, 16, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866834 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 Building ZINC001294866834 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294866834 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 907) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294866834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866834 none Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 16, 16, 16, 10, 8, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 12, 12, 50, 50, 50, 50, 50, 37, 37, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 908) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294866834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294866834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294866834 none Cc1cncn1CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 16, 16, 16, 6, 4, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 35, 35, 16, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294866834 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294866834 Building ZINC001294867462 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867462 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/909 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867462 none CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 48, 26, 26, 16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 20, 20, 48, 49, 49, 49, 49, 49, 49, 49, 26, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/910 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867462 none CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 36, 25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867462 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 Building ZINC001294867462 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867462 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 909) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867462 none CC[C@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 48, 26, 26, 16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 20, 20, 48, 49, 49, 49, 49, 49, 49, 49, 26, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 910) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867462 none CC[C@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 36, 25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867462 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867462 Building ZINC001294867463 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867463 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/911 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867463 none CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 30, 46, 30, 30, 15, 8, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 17, 17, 46, 50, 50, 47, 47, 47, 47, 47, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/912 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867463 none CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 49, 33, 33, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 22, 22, 49, 50, 50, 49, 49, 49, 49, 49, 33, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867463 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 Building ZINC001294867463 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867463 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 911) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867463 none CC[C@@H](C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 30, 46, 30, 30, 15, 8, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 17, 17, 46, 50, 50, 47, 47, 47, 47, 47, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 912) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867463 none CC[C@@H](C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 49, 33, 33, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 22, 22, 49, 50, 50, 49, 49, 49, 49, 49, 33, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867463 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867463 Building ZINC001294867464 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867464 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/913 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867464 none CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 38, 49, 38, 38, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 26, 26, 49, 50, 50, 49, 49, 49, 49, 49, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/914 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867464 none CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 32, 47, 32, 32, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 16, 16, 47, 50, 50, 48, 48, 48, 48, 48, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867464 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 Building ZINC001294867464 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867464 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 913) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867464 none CC[C@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 38, 49, 38, 38, 24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 26, 26, 49, 50, 50, 49, 49, 49, 49, 49, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 914) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867464 none CC[C@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 32, 47, 32, 32, 15, 9, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 16, 16, 47, 50, 50, 48, 48, 48, 48, 48, 32, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867464 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867464 Building ZINC001294867465 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867465 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/915 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867465 none CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 34, 34, 24, 14, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/916 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867465 none CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 28, 47, 28, 28, 18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 47, 49, 49, 48, 48, 48, 48, 48, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867465 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 Building ZINC001294867465 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867465 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 915) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867465 none CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 34, 34, 24, 14, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 916) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C) `ZINC001294867465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294867465 none CC[C@@H](C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)N(C)C 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', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 10, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 28, 47, 28, 28, 18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 23, 23, 47, 49, 49, 48, 48, 48, 48, 48, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867465 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867465 Building ZINC001294867900 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867900 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/917 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867900 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 15, 24, 24, 34, 49, 49, 49, 49, 49, 49, 15, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/918 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867900 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 23, 23, 30, 30, 40, 50, 50, 50, 50, 50, 50, 23, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867900 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 Building ZINC001294867900 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867900 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 917) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867900 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 15, 15, 24, 24, 34, 49, 49, 49, 49, 49, 49, 15, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 918) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867900 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 23, 23, 30, 30, 40, 50, 50, 50, 50, 50, 50, 23, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 30, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867900 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867900 Building ZINC001294867901 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867901 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/919 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867901 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 22, 22, 29, 29, 33, 50, 50, 50, 50, 50, 50, 22, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/920 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867901 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 27, 27, 38, 50, 50, 50, 50, 50, 50, 16, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867901 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 Building ZINC001294867901 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294867901 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 919) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294867901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867901 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 22, 22, 29, 29, 33, 50, 50, 50, 50, 50, 50, 22, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 920) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1) `ZINC001294867901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294867901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294867901 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@]1(C)CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 27, 27, 38, 50, 50, 50, 50, 50, 50, 16, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294867901 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294867901 Building ZINC001294868138 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868138 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/921 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868138 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 20, 25, 25, 25, 46, 49, 50, 50, 50, 50, 50, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 46, 46, 49, 49, 50, 50, 20, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/922 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868138 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 14, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 14, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 46, 46, 50, 50, 50, 50, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868138 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 Building ZINC001294868138 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868138 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 921) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868138 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 20, 20, 25, 25, 25, 46, 49, 50, 50, 50, 50, 50, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 46, 46, 49, 49, 50, 50, 20, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 922) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868138 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 14, 14, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 14, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 22, 46, 46, 50, 50, 50, 50, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868138 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868138 Building ZINC001294868139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/923 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 12, 17, 17, 17, 44, 50, 50, 50, 50, 50, 50, 12, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 44, 44, 50, 50, 50, 50, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/924 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 13, 18, 18, 18, 46, 50, 50, 50, 50, 50, 50, 13, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 46, 46, 50, 50, 50, 50, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 Building ZINC001294868139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 923) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 12, 12, 17, 17, 17, 44, 50, 50, 50, 50, 50, 50, 12, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 44, 44, 50, 50, 50, 50, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 924) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1) `ZINC001294868139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1cn[nH]c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 8, 6, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 13, 18, 18, 18, 46, 50, 50, 50, 50, 50, 50, 13, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 46, 46, 50, 50, 50, 50, 16, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868139 Building ZINC001294868232 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868232 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/925 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868232 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 6, 10, 10, 15, 15, 15, 42, 47, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 15, 42, 42, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/926 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868232 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 4, 7, 7, 12, 12, 12, 37, 47, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 37, 37, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868232 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 Building ZINC001294868232 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868232 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 925) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868232 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 6, 10, 10, 15, 15, 15, 42, 47, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 15, 42, 42, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 926) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868232 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 4, 7, 7, 12, 12, 12, 37, 47, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 37, 37, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868232 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868232 Building ZINC001294868235 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868235 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/927 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868235 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 6, 10, 10, 14, 14, 14, 37, 46, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 37, 37, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/928 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868235 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 9, 14, 14, 15, 15, 15, 37, 48, 50, 50, 50, 50, 50, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 37, 37, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868235 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 Building ZINC001294868235 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868235 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 927) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868235 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 6, 10, 10, 14, 14, 14, 37, 46, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 37, 37, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 928) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1) `ZINC001294868235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868235 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 9, 14, 14, 15, 15, 15, 37, 48, 50, 50, 50, 50, 50, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 37, 37, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868235 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868235 Building ZINC001294868237 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868237 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/929 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868237 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 8, 13, 13, 17, 17, 17, 40, 48, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 40, 40, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/930 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868237 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 7, 10, 10, 15, 15, 15, 37, 49, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 37, 37, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868237 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 Building ZINC001294868237 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868237 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 929) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868237 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 8, 13, 13, 17, 17, 17, 40, 48, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 40, 40, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 930) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868237 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 7, 10, 10, 15, 15, 15, 37, 49, 50, 50, 50, 50, 50, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 15, 37, 37, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868237 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868237 Building ZINC001294868239 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868239 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/931 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868239 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 7, 10, 10, 10, 10, 10, 30, 47, 50, 50, 50, 50, 50, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 30, 30, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/932 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868239 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 5, 11, 11, 13, 13, 13, 37, 48, 50, 50, 50, 50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 13, 37, 37, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868239 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 Building ZINC001294868239 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868239 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 931) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868239 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 7, 10, 10, 10, 10, 10, 30, 47, 50, 50, 50, 50, 50, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 10, 30, 30, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 932) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1) `ZINC001294868239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294868239 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CO[C@H]1CCOC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 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, 2, 5, 11, 11, 13, 13, 13, 37, 48, 50, 50, 50, 50, 50, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 13, 37, 37, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868239 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868239 Building ZINC001294868329 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868329 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/933 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868329 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 42, 42, 42, 28, 10, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 30, 30, 50, 50, 50, 50, 50, 50, 50, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 150] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 335 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/934 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868329 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 36, 36, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 31, 31, 50, 50, 50, 50, 50, 50, 50, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 150] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 342 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868329 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 Building ZINC001294868329 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868329 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 933) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868329 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 42, 42, 42, 28, 10, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 30, 30, 50, 50, 50, 50, 50, 50, 50, 42, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 150] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 335 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 934) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868329 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 36, 36, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 31, 31, 50, 50, 50, 50, 50, 50, 50, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 150] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 342 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868329 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868329 Building ZINC001294868330 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868330 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/935 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868330 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 38, 38, 38, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 30, 30, 49, 49, 49, 49, 49, 49, 49, 38, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 147] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 326 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/936 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868330 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 38, 38, 38, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 30, 30, 50, 50, 50, 50, 50, 50, 50, 38, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 150] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868330 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 Building ZINC001294868330 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868330 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 935) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868330 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 38, 38, 38, 26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 30, 30, 49, 49, 49, 49, 49, 49, 49, 38, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 147] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 326 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 936) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O) `ZINC001294868330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001294868330 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 38, 38, 38, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 30, 30, 50, 50, 50, 50, 50, 50, 50, 38, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 150] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 339 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868330 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868330 Building ZINC001294868809 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868809 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/937 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868809 none CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 32, 32, 32, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 49, 49, 49, 49, 49, 49, 49, 49, 32, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/938 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868809 none CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 34, 34, 34, 24, 11, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 27, 27, 50, 50, 50, 50, 50, 50, 48, 48, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868809 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 Building ZINC001294868809 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868809 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 937) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868809 none CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 32, 32, 32, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 49, 49, 49, 49, 49, 49, 49, 49, 32, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 938) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868809 none CC(=O)N(C)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 48, 50, 34, 34, 34, 24, 11, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 27, 27, 50, 50, 50, 50, 50, 50, 48, 48, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868809 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868809 Building ZINC001294868810 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868810 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/939 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868810 none CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 30, 30, 30, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 50, 50, 50, 50, 50, 50, 49, 49, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/940 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868810 none CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 36, 36, 36, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 50, 50, 50, 49, 49, 49, 49, 49, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868810 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 Building ZINC001294868810 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294868810 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 939) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294868810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868810 none CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 30, 30, 30, 20, 11, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 50, 50, 50, 50, 50, 50, 49, 49, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 940) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294868810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294868810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001294868810 none CC(=O)N(C)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 36, 36, 36, 21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 26, 26, 50, 50, 50, 49, 49, 49, 49, 49, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294868810 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294868810 Building ZINC001294869707 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294869707 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/941 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294869707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869707 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 17, 26, 26, 26, 48, 50, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 48, 48, 50, 50, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/942 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294869707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869707 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 31, 31, 31, 46, 50, 50, 50, 50, 50, 50, 19, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 46, 46, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294869707 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 Building ZINC001294869707 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294869707 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 941) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294869707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869707 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 17, 17, 26, 26, 26, 48, 50, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 48, 48, 50, 50, 50, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 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/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 942) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294869707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869707 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 31, 31, 31, 46, 50, 50, 50, 50, 50, 50, 19, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 46, 46, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294869707 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869707 Building ZINC001294869708 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294869708 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/943 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869708.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294869708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869708 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 19, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 48, 48, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/944 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869708.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294869708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869708 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 26, 26, 26, 48, 50, 50, 50, 50, 50, 50, 19, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 48, 48, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294869708 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 Building ZINC001294869708 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294869708 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 943) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869708.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294869708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869708 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 19, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 27, 48, 48, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 944) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1) `ZINC001294869708.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294869708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294869708 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)Cn1ccccc1=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 19, 19, 26, 26, 26, 48, 50, 50, 50, 50, 50, 50, 19, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 26, 48, 48, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294869708 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294869708 Building ZINC001294878405 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294878405 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/945 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294878405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878405 none Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 26, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 50, 50, 50, 50, 50, 50, 42, 26, 26, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50] 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, 48]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/946 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294878405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878405 none Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 44, 44, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 50, 50, 50, 50, 50, 50, 44, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50] 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, 48]) total number of confs: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294878405 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 Building ZINC001294878405 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294878405 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 945) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294878405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878405 none Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 26, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 50, 50, 50, 50, 50, 50, 42, 26, 26, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50] 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, 48]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 946) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294878405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878405 none Cn1ncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 44, 44, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 50, 50, 50, 50, 50, 50, 44, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50] 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, 48]) total number of confs: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294878405 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878405 Building ZINC001294878406 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294878406 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/947 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294878406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878406 none Cn1ncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 50, 50, 50, 50, 50, 50, 42, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50] 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, 48]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/948 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294878406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878406 none Cn1ncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 42, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50] 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, 48]) total number of confs: 182 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294878406 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 Building ZINC001294878406 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294878406 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 947) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294878406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878406 none Cn1ncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 50, 50, 50, 50, 50, 50, 42, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 50, 50] 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, 48]) total number of confs: 183 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 948) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N) `ZINC001294878406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294878406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001294878406 none Cn1ncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)c1N 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 42, 42, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 42, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50] 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, 48]) total number of confs: 182 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294878406 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294878406 Building ZINC001294881878 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294881878 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/949 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294881878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881878 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 20, 20, 20, 42, 49, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 42, 42, 49, 49, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/950 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294881878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881878 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 18, 18, 18, 45, 46, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 45, 45, 46, 46, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294881878 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 Building ZINC001294881878 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294881878 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 949) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294881878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881878 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 20, 20, 20, 42, 49, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 20, 42, 42, 49, 49, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 950) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294881878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881878 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 18, 18, 18, 45, 46, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 18, 45, 45, 46, 46, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294881878 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881878 Building ZINC001294881879 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294881879 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/951 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294881879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881879 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 18, 18, 18, 48, 50, 50, 50, 50, 50, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 48, 48, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/952 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294881879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881879 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 8, 16, 16, 16, 40, 47, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 16, 40, 40, 47, 47, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294881879 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 Building ZINC001294881879 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294881879 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 951) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294881879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881879 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 18, 18, 18, 48, 50, 50, 50, 50, 50, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 48, 48, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 952) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1) `ZINC001294881879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294881879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294881879 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCn1ccnn1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 8, 16, 16, 16, 40, 47, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 16, 40, 40, 47, 47, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294881879 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294881879 Building ZINC001294889487 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889487 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/953 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889487 none C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 26, 26, 26, 17, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/954 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889487 none C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 36, 49, 24, 24, 24, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 49, 50, 50, 50, 49, 49, 49, 36, 36, 24, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50] 50 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: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889487 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 Building ZINC001294889487 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889487 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 953) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889487 none C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 26, 26, 26, 17, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 44, 44, 26, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 954) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889487 none C[C@@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 36, 49, 24, 24, 24, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 49, 50, 50, 50, 49, 49, 49, 36, 36, 24, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 50, 50, 50] 50 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: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889487 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889487 Building ZINC001294889489 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889489 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/955 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889489 none C[C@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 22, 22, 22, 13, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 35, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50] 50 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/956 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889489 none C[C@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 24, 24, 24, 16, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 50, 50, 50, 50, 50, 50, 50, 38, 38, 24, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50] 50 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: 235 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889489 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 Building ZINC001294889489 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889489 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 955) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889489 none C[C@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 22, 22, 22, 13, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 35, 35, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50] 50 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: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 956) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889489 none C[C@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 24, 24, 24, 16, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 50, 50, 50, 50, 50, 50, 50, 38, 38, 24, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50] 50 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: 235 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889489 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889489 Building ZINC001294889490 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889490 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/957 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889490 none C[C@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 22, 22, 22, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 34, 34, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/958 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889490 none C[C@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 33, 49, 21, 21, 21, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 49, 50, 50, 50, 49, 49, 49, 33, 33, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889490 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 Building ZINC001294889490 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889490 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 957) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889490 none C[C@H](CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 50, 22, 22, 22, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 50, 34, 34, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 958) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889490 none C[C@H](CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 33, 49, 21, 21, 21, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 49, 50, 50, 50, 49, 49, 49, 33, 33, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889490 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889490 Building ZINC001294889491 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889491 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/959 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889491 none C[C@@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 30, 49, 17, 17, 17, 13, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 49, 50, 50, 50, 49, 49, 49, 30, 30, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/960 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/960' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889491 none C[C@@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 22, 22, 22, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 48, 50, 50, 50, 48, 48, 48, 34, 34, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50] 50 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: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889491 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 Building ZINC001294889491 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294889491 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 959) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294889491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889491 none C[C@@H](CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 30, 49, 17, 17, 17, 13, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 49, 50, 50, 50, 49, 49, 49, 30, 30, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50] 50 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: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 960) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O) `ZINC001294889491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294889491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001294889491 none C[C@@H](CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 22, 22, 22, 13, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 48, 50, 50, 50, 48, 48, 48, 34, 34, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50, 50, 50] 50 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: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294889491 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294889491 Building ZINC001294894138 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294894138 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/961 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294894138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894138 none Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 40, 40, 40, 24, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 50, 50, 50, 50, 50, 49, 49, 40, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/962 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294894138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894138 none Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 41, 25, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 11, 11, 50, 50, 50, 50, 50, 50, 50, 41, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 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: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294894138 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 Building ZINC001294894138 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294894138 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 961) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294894138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894138 none Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 40, 40, 40, 24, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 14, 14, 50, 50, 50, 50, 50, 49, 49, 40, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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: 216 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 962) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294894138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894138 none Cc1ccnn1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 41, 25, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 11, 11, 50, 50, 50, 50, 50, 50, 50, 41, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 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: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294894138 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894138 Building ZINC001294894139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294894139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/963 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294894139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894139 none Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 43, 43, 24, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 50, 50, 50, 50, 50, 50, 50, 43, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/964 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294894139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894139 none Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 40, 40, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 50, 50, 50, 50, 50, 50, 50, 40, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294894139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 Building ZINC001294894139 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294894139 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 963) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294894139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894139 none Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 43, 43, 24, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 50, 50, 50, 50, 50, 50, 50, 43, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 964) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294894139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294894139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294894139 none Cc1ccnn1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 40, 40, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 50, 50, 50, 50, 50, 50, 50, 40, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 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: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294894139 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294894139 Building ZINC001294902368 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902368 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/965 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902368 none CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 29, 23, 29, 29, 23, 23, 13, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 39, 29, 29, 29, 23, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/966 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902368 none CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 31, 26, 31, 31, 26, 26, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 42, 31, 31, 31, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902368 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 Building ZINC001294902368 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902368 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 965) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902368 none CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 29, 23, 29, 29, 23, 23, 13, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 39, 29, 29, 29, 23, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 966) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902368 none CCC(=O)N[C@@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 31, 26, 31, 31, 26, 26, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 42, 31, 31, 31, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902368 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902368 Building ZINC001294902369 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902369 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/967 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902369 none CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 27, 27, 27, 27, 27, 27, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 50, 50, 50, 50, 50, 37, 27, 27, 27, 27, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/968 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902369 none CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 27, 25, 27, 27, 25, 25, 13, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 50, 50, 50, 50, 50, 38, 27, 27, 27, 25, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902369 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 Building ZINC001294902369 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902369 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 967) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902369 none CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 27, 27, 27, 27, 27, 27, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 8, 8, 50, 50, 50, 50, 50, 37, 27, 27, 27, 27, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 228 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 968) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902369 none CCC(=O)N[C@@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 27, 25, 27, 27, 25, 25, 13, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 50, 50, 50, 50, 50, 38, 27, 27, 27, 25, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 226 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902369 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902369 Building ZINC001294902370 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902370 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/969 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902370 none CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 29, 25, 29, 29, 25, 25, 14, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 40, 29, 29, 29, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/970 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902370 none CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 25, 22, 25, 25, 22, 22, 13, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 38, 25, 25, 25, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902370 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 Building ZINC001294902370 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902370 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 969) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902370 none CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 29, 25, 29, 29, 25, 25, 14, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 9, 9, 50, 50, 50, 50, 50, 40, 29, 29, 29, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 970) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902370 none CCC(=O)N[C@H](C)C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 25, 22, 25, 25, 22, 22, 13, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 38, 25, 25, 25, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 222 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902370 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902370 Building ZINC001294902371 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902371 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/971 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902371 none CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 29, 26, 29, 29, 26, 26, 15, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 39, 29, 29, 29, 26, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/972 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902371 none CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 30, 28, 30, 30, 28, 28, 15, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 38, 30, 30, 30, 28, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902371 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 Building ZINC001294902371 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294902371 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 971) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294902371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902371 none CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 29, 26, 29, 29, 26, 26, 15, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 39, 29, 29, 29, 26, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 223 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 972) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294902371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294902371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001294902371 none CCC(=O)N[C@H](C)C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 30, 28, 30, 30, 28, 28, 15, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 38, 30, 30, 30, 28, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 224 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294902371 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294902371 Building ZINC001294905847 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905847 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/973 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/974 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/975 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/975' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/976 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/976' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905847 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 Building ZINC001294905847 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905847 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 973) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 974) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 975) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 976) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905847 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 Building ZINC001294905847 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905847 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 973) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 974) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 975) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 976) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905847 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 Building ZINC001294905847 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905847 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 973) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 974) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 975) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 16, 30, 30, 35, 50, 50, 50, 50, 50, 50, 50, 8, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 976) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905847.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905847 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 18, 28, 28, 33, 50, 50, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905847 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905847 Building ZINC001294905848 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905848 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/977 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/978 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/979 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/979' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/980 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/980' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905848 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 Building ZINC001294905848 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905848 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 977) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 978) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 979) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 980) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905848 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 Building ZINC001294905848 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905848 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 977) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 978) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 979) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 980) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905848 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 Building ZINC001294905848 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001294905848 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 977) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 978) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `2' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 2 (index: 979) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `3' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 3 (index: 980) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001294905848.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001294905848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294905848 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 18, 31, 31, 35, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294905848 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 3: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/3.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/0.* 2: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848/2.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294905848 Building ZINC001294908484 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908484 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/981 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908484 none CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 32, 32, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 32, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50] 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, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/982 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908484 none CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 18, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 33, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50, 50] 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, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908484 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 Building ZINC001294908484 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908484 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 981) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908484 none CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 32, 32, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 32, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50] 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, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 982) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908484 none CNC(=O)C1(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 33, 33, 18, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 50, 33, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 50, 50, 50, 50] 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, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908484 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908484 Building ZINC001294908485 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908485 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/983 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908485 none CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 19, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 49, 49, 49, 49, 49, 49, 32, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 49, 49, 49, 49] 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, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/984 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908485 none CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 16, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 36, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50] 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, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908485 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 Building ZINC001294908485 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908485 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 983) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908485 none CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 19, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 49, 49, 49, 49, 49, 49, 32, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 49, 49, 49, 49] 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, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 984) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1) `ZINC001294908485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001294908485 none CNC(=O)C1(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 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, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 36, 36, 16, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 50, 36, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50] 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, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908485 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908485 Building ZINC001294908923 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908923 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/985 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908923 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 3, 3, 8, 17, 17, 17, 46, 49, 49, 49, 49, 49, 49, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 44, 44, 49, 49, 49, 49, 49, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/986 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908923 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 47, 50, 50, 50, 50, 50, 50, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 44, 44, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908923 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 Building ZINC001294908923 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908923 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 985) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908923 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 3, 3, 8, 17, 17, 17, 46, 49, 49, 49, 49, 49, 49, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 44, 44, 49, 49, 49, 49, 49, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 986) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908923 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 47, 50, 50, 50, 50, 50, 50, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 44, 44, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908923 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908923 Building ZINC001294908924 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908924 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/987 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908924 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 20, 20, 20, 47, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 44, 44, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/988 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908924 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 3, 3, 8, 18, 18, 18, 46, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 44, 44, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908924 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 Building ZINC001294908924 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908924 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 987) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908924 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 20, 20, 20, 47, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 44, 44, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 988) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908924 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 3, 3, 8, 18, 18, 18, 46, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 44, 44, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908924 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908924 Building ZINC001294908925 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908925 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/989 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908925 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 9, 17, 17, 17, 48, 50, 50, 50, 50, 50, 50, 4, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 45, 45, 50, 50, 50, 50, 50, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/990 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908925 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 8, 18, 18, 18, 46, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 42, 42, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908925 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 Building ZINC001294908925 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908925 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 989) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908925 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 9, 17, 17, 17, 48, 50, 50, 50, 50, 50, 50, 4, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 45, 45, 50, 50, 50, 50, 50, 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]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 990) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1) `ZINC001294908925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908925 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C[C@@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 8, 18, 18, 18, 46, 50, 50, 50, 50, 50, 50, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 18, 42, 42, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908925 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908925 Building ZINC001294908926 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908926 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/991 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908926 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 19, 19, 19, 46, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 43, 43, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/992 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908926 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 9, 17, 17, 17, 49, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 45, 45, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908926 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 Building ZINC001294908926 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294908926 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 991) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294908926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908926 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 19, 19, 19, 46, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 43, 43, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 992) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1) `ZINC001294908926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294908926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001294908926 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C[C@H]1CCC(=O)N1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of 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, 4, 4, 9, 17, 17, 17, 49, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 45, 45, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294908926 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294908926 Building ZINC001294912592 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294912592 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/993 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294912592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912592 none Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 47, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 49, 49, 49, 147, 49, 47, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 328 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/994 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294912592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912592 none Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations 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, 49, 49, 49, 25, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 10, 10, 50, 50, 50, 150, 50, 49, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294912592 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 Building ZINC001294912592 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294912592 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 993) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294912592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912592 none Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 47, 24, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 12, 12, 49, 49, 49, 147, 49, 47, 24, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 328 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 994) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294912592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912592 none Cn1c(O)ncc1C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations 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, 49, 49, 49, 25, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 10, 10, 50, 50, 50, 150, 50, 49, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294912592 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912592 Building ZINC001294912594 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294912594 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/995 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294912594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912594 none Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations 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, 47, 47, 47, 25, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 50, 50, 50, 150, 50, 47, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 346 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/996 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294912594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912594 none Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 47, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 49, 49, 49, 147, 49, 47, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 330 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294912594 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 Building ZINC001294912594 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294912594 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 995) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294912594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912594 none Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations 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, 47, 47, 47, 25, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 50, 50, 50, 150, 50, 47, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 346 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 996) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294912594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294912594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001294912594 none Cn1c(O)ncc1C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'O.3', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 47, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 49, 49, 49, 147, 49, 47, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 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, 43, 44, 45, 46, 47]) total number of confs: 330 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294912594 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294912594 Building ZINC001294913455 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294913455 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/997 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294913455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913455 none Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 38, 38, 38, 25, 11, 3, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 14, 14, 49, 49, 49, 49, 49, 49, 38, 25, 25, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/998 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294913455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913455 none Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 50, 50, 50, 50, 50, 50, 31, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294913455 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 Building ZINC001294913455 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294913455 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 997) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294913455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913455 none Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 38, 38, 38, 25, 11, 3, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 14, 14, 49, 49, 49, 49, 49, 49, 38, 25, 25, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 998) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294913455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913455 none Cc1nc[nH]c1CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 50, 50, 50, 50, 50, 50, 31, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294913455 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913455 Building ZINC001294913456 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294913456 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/999 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294913456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913456 none Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 35, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/13323/xbn-8058097.40/working/3D/1000 `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294913456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913456 none Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 48, 33, 33, 33, 20, 9, 3, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 13, 13, 49, 49, 49, 49, 48, 48, 33, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294913456 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 Building ZINC001294913456 mkdir: created directory `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001294913456 mkdir: created directory `0' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/0 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 0 (index: 999) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001294913456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913456 none Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 35, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 mkdir: created directory `1' /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/1 /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Protomer 1 (index: 1000) grep: /scratch/xiaobo/13323/xbn-8058097.40/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001294913456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001294913456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001294913456 none Cc1nc[nH]c1CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 6, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 48, 33, 33, 33, 20, 9, 3, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 13, 13, 49, 49, 49, 49, 48, 48, 33, 20, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Finished preparing ZINC001294913456 Recording results /scratch/xiaobo/13323/xbn-8058097.40/working /scratch/xiaobo/13323/xbn-8058097.40 Appending to /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.* 1: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/1.* 0: /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456/0.* Removing working files in /scratch/xiaobo/13323/xbn-8058097.40/working/building/ZINC001294913456 /scratch/xiaobo/13323/xbn-8058097.40 Compressing combined databse files /scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/13323/xbn-8058097.40/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/13323/xbn-8058097.40/working/3D/1001' removed directory: `/scratch/xiaobo/13323/xbn-8058097.40/working/3D' rmdir: removing directory, `/scratch/xiaobo/13323/xbn-8058097.40/working/building' rmdir: removing directory, `/scratch/xiaobo/13323/xbn-8058097.40/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs `/scratch/xiaobo/13323/xbn-8058097.40' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbn' `/scratch/xiaobo/13323/xbn-8058097.40/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbn/finished' `/scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xbn/finished/xbn.db2.gz' removed `/scratch/xiaobo/13323/xbn-8058097.40/finished/xbn.db2.gz' removed directory: `/scratch/xiaobo/13323/xbn-8058097.40/finished' removed directory: `/scratch/xiaobo/13323/xbn-8058097.40'